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- PDB-3d4g: ZP-N domain of mammalian sperm receptor ZP3 (crystal form II) -

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Basic information

Entry
Database: PDB / ID: 3d4g
TitleZP-N domain of mammalian sperm receptor ZP3 (crystal form II)
ComponentsMaltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
KeywordsCELL ADHESION / fertilization / oocyte / egg coat / zona pellucida / vitelline envelope / ZP domain / egg-sperm interaction / species-specific gamete recognition / speciation / biodiversity / infertility / extracellular matrix / immunoglobulin-like fold / glycoprotein / receptor / secreted / transmembrane
Function / homology
Function and homology information


positive regulation of type IV hypersensitivity / positive regulation of acrosomal vesicle exocytosis / positive regulation of antral ovarian follicle growth / Interaction With Cumulus Cells And The Zona Pellucida / egg coat formation / positive regulation of humoral immune response / structural constituent of egg coat / egg coat / acrosin binding / negative regulation of binding of sperm to zona pellucida ...positive regulation of type IV hypersensitivity / positive regulation of acrosomal vesicle exocytosis / positive regulation of antral ovarian follicle growth / Interaction With Cumulus Cells And The Zona Pellucida / egg coat formation / positive regulation of humoral immune response / structural constituent of egg coat / egg coat / acrosin binding / negative regulation of binding of sperm to zona pellucida / positive regulation of acrosome reaction / positive regulation of ovarian follicle development / binding of sperm to zona pellucida / humoral immune response mediated by circulating immunoglobulin / oocyte development / blastocyst formation / regulation of signaling receptor activity / positive regulation of leukocyte migration / detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / positive regulation of interleukin-4 production / positive regulation of T cell proliferation / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / extracellular matrix / positive regulation of inflammatory response / positive regulation of type II interferon production / outer membrane-bounded periplasmic space / carbohydrate binding / collagen-containing extracellular matrix / periplasmic space / receptor ligand activity / negative regulation of DNA-templated transcription / DNA damage response / positive regulation of DNA-templated transcription / extracellular space / membrane / identical protein binding / plasma membrane
Similarity search - Function
Zona pellucida, ZP-N domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein ...Zona pellucida, ZP-N domain / : / Zona pellucida domain, conserved site / Zona pellucida, ZP-C domain / ZP domain signature. / Zona pellucida-like domain / Zona pellucida (ZP) domain / ZP domain profile. / Zona pellucida domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Zona pellucida sperm-binding protein 3
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJovine, L. / Monne, M.
Citation
Journal: Nature / Year: 2008
Title: Crystal structure of the ZP-N domain of ZP3 reveals the core fold of animal egg coats
Authors: Monne, M. / Han, L. / Schwend, T. / Burendahl, S. / Jovine, L.
#1: Journal: CELL(CAMBRIDGE,MASS.) / Year: 1980
Title: Mammalian sperm-egg interaction: identification of a glycoprotein in mouse egg zonae pellucidae possessing receptor activity for sperm
Authors: Bleil, J.D. / Wassarman, P.M.
#2: Journal: Febs Lett. / Year: 1992
Title: A large domain common to sperm receptors (Zp2 and Zp3) and TGF-beta type III receptor
Authors: Bork, P. / Sander, C.
#3: Journal: Nat Cell Biol / Year: 2002
Title: The ZP domain is a conserved module for polymerization of extracellular proteins.
Authors: Luca Jovine / Huayu Qi / Zev Williams / Eveline Litscher / Paul M Wassarman /
Abstract: Many eukaryotic extracellular proteins share a sequence of unknown function, called the zona pellucida (ZP) domain. Among these proteins are the mammalian sperm receptors ZP2 and ZP3, non-mammalian ...Many eukaryotic extracellular proteins share a sequence of unknown function, called the zona pellucida (ZP) domain. Among these proteins are the mammalian sperm receptors ZP2 and ZP3, non-mammalian egg coat proteins, Tamm-Horsfall protein (THP), glycoprotein-2 (GP-2), alpha- and beta-tectorins, transforming growth factor (TGF)-beta receptor III and endoglin, DMBT-1 (deleted in malignant brain tumour-1), NompA (no-mechanoreceptor-potential-A), Dumpy and cuticlin-1 (refs 1,2). Here, we report that the ZP domain of ZP2, ZP3 and THP is responsible for polymerization of these proteins into filaments of similar supramolecular structure. Most ZP domain proteins are synthesized as precursors with carboxy-terminal transmembrane domains or glycosyl phosphatidylinositol (GPI) anchors. Our results demonstrate that the C-terminal transmembrane domain and short cytoplasmic tail of ZP2 and ZP3 are not required for secretion, but are essential for assembly. Finally, we suggest a molecular basis for dominant human hearing disorders caused by point mutations within the ZP domain of alpha-tectorin.
#4: Journal: Proc Natl Acad Sci U S A / Year: 2004
Title: A duplicated motif controls assembly of zona pellucida domain proteins.
Authors: Luca Jovine / Huayu Qi / Zev Williams / Eveline S Litscher / Paul M Wassarman /
Abstract: Many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer polymerize into filaments and extracellular matrices through zona pellucida (ZP) ...Many secreted eukaryotic glycoproteins that play fundamental roles in development, hearing, immunity, and cancer polymerize into filaments and extracellular matrices through zona pellucida (ZP) domains. ZP domain proteins are synthesized as precursors containing C-terminal propeptides that are cleaved at conserved sites. However, the consequences of this processing and the mechanism by which nascent proteins assemble are unclear. By microinjection of mutated DNA constructs into growing oocytes and mammalian cell transfection, we have identified a conserved duplicated motif [EHP (external hydrophobic patch)/IHP (internal hydrophobic patch)] regulating the assembly of mouse ZP proteins. Whereas the transmembrane domain (TMD) of ZP3 can be functionally replaced by an unrelated TMD, mutations in either EHP or IHP do not hinder secretion of full-length ZP3 but completely abolish its assembly. Because mutants truncated before the TMD are not processed, we conclude that the conserved TMD of mammalian ZP proteins does not engage them in specific interactions but is essential for C-terminal processing. Cleavage of ZP precursors results in loss of the EHP, thereby activating secreted polypeptides to assemble by using the IHP within the ZP domain. Taken together, these findings suggest a general mechanism for assembly of ZP domain proteins.
#5: Journal: Annu Rev Biochem / Year: 2005
Title: Zona pellucida domain proteins.
Authors: Luca Jovine / Costel C Darie / Eveline S Litscher / Paul M Wassarman /
Abstract: Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to ...Many eukaryotic proteins share a sequence designated as the zona pellucida (ZP) domain. This structural element, present in extracellular proteins from a wide variety of organisms, from nematodes to mammals, consists of approximately 260 amino acids with eight conserved cysteine (Cys) residues and is located close to the C terminus of the polypeptide. ZP domain proteins are often glycosylated, modular structures consisting of multiple types of domains. Predictions can be made about some of the structural features of the ZP domain and ZP domain proteins. The functions of ZP domain proteins vary tremendously, from serving as structural components of egg coats, appendicularian mucous houses, and nematode dauer larvae, to serving as mechanotransducers in flies and receptors in mammals and nonmammals. Generally, ZP domain proteins are present in filaments and/or matrices, which is consistent with the role of the domain in protein polymerization. A general mechanism for assembly of ZP domain proteins has been presented. It is likely that the ZP domain plays a common role despite its presence in proteins of widely diverse functions.
#6: Journal: Bmc Biochem. / Year: 2006
Title: The PLAC1-homology region of the ZP domain is sufficient for protein polymerisation
Authors: Jovine, L. / Janssen, W.G. / Litscher, E.S. / Wassarman, P.M.
History
DepositionMay 14, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
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Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id / _struct_ref_seq_dif.details
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Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED
Remark 40MOLPROBITY STRUCTURE VALIDATION PROGRAMS: MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS: I.W.DAVIS,V. ...MOLPROBITY STRUCTURE VALIDATION PROGRAMS: MOLPROBITY (KING, REDUCE, AND PROBE) AUTHORS: I.W.DAVIS,V.B.CHEN, R.M.IMMORMINO, J.J.HEADD,W.B.ARENDALL,J.M.WORD AUTHORS: I.W.DAVIS,A.LEAVER-FAY,V.B.CHEN,J.N.BLOCK, G.J.KAPRAL,X.WANG,L.W.MURRAY,W.B.ARENDALL, J.SNOEYINK,J.S.RICHARDSON,D.C.RICHARDSON REFERENCE: MOLPROBITY: ALL-ATOM CONTACTS AND STRUCTURE VALIDATION FOR PROTEINS AND NUCLEIC ACIDS NUCLEIC ACIDS RESEARCH. 2007;35:W375-83.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
B: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
C: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
D: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
E: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
F: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
G: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
H: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)427,29240
Polymers423,5928
Non-polymers3,70032
Water34,8411934
1
A: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4115
Polymers52,9491
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4115
Polymers52,9491
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4115
Polymers52,9491
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4115
Polymers52,9491
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4115
Polymers52,9491
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4115
Polymers52,9491
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4115
Polymers52,9491
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4115
Polymers52,9491
Non-polymers4634
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.050, 91.960, 140.480
Angle α, β, γ (deg.)89.99, 90.18, 89.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3 / Maltose-binding protein/ZP3 ZP-N domain chimera / MBP / Zona pellucida glycoprotein ZP3 / Sperm ...Maltose-binding protein/ZP3 ZP-N domain chimera / MBP / Zona pellucida glycoprotein ZP3 / Sperm receptor / Zona pellucida protein C


Mass: 52948.945 Da / Num. of mol.: 8
Fragment: ZP3 ZP-N domain, UNP residues 27-393, UNP residues 42-143
Mutation: I3T, E360A, K363A, D364A, R368N
Source method: isolated from a genetically manipulated source
Details: This protein is a chimera. Residues 2-368 are from E. COLI maltose binding protein (MBP), correspond to residues 27-393 of swiss-prot database entry P0AEX9 and contain mutations I3T, E360A, ...Details: This protein is a chimera. Residues 2-368 are from E. COLI maltose binding protein (MBP), correspond to residues 27-393 of swiss-prot database entry P0AEX9 and contain mutations I3T, E360A, K363A, D364A, R368N (corresponding to I28T, E385A, K388A, D389A AND R393N in P0AEX9). Residues 372-473 are from mouse ZP3 protein and correspond to residues 42-143 of swiss-prot database entry P10761.
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Mus musculus (house mouse)
Cellular location: Extracellular matrix / Gene: Zp3, Zp-3, Zpc / Plasmid: PLJMBP4C, PLJDIS1 / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (DE3) / References: UniProt: P0AEX9, UniProt: P10761
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1934 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Sample: 15mg/ml protein in 0.05M sodium chloride, 0.01M Tris-HCL, PH7.2, 0.001M maltose. Reservoir: 10% PEG6000, 0.2M calcium chloride, 0.1M Tris-HCL, PH7.0. Sample to reservoir ratio in ...Details: Sample: 15mg/ml protein in 0.05M sodium chloride, 0.01M Tris-HCL, PH7.2, 0.001M maltose. Reservoir: 10% PEG6000, 0.2M calcium chloride, 0.1M Tris-HCL, PH7.0. Sample to reservoir ratio in drop: 1:1, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535 / Wavelength: 0.9535 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 7, 2006
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.3→500 Å / Num. all: 202456 / Num. obs: 193240 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 48.357 Å2 / Rsym value: 0.05 / Net I/σ(I): 11
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.6 / Num. unique all: 12935 / Rsym value: 0.529 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.3.0038refinement
MxCuBEdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D4C

3d4c


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 15.285 / SU ML: 0.196 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2139 1.1 %RANDOM
Rwork0.2014 ---
obs0.2017 193225 95.45 %-
all-202438 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å2-0.06 Å2-0.65 Å2
2--0.97 Å2-0.08 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29088 0 208 1934 31230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02230000
X-RAY DIFFRACTIONr_bond_other_d00.0220125
X-RAY DIFFRACTIONr_angle_refined_deg0.9271.97840741
X-RAY DIFFRACTIONr_angle_other_deg4.2073.00249185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.52553759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35725.2721286
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.755154960
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.97415112
X-RAY DIFFRACTIONr_chiral_restr0.0510.24584
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0233225
X-RAY DIFFRACTIONr_gen_planes_other0.0030.025655
X-RAY DIFFRACTIONr_nbd_refined0.1770.26182
X-RAY DIFFRACTIONr_nbd_other0.2170.219936
X-RAY DIFFRACTIONr_nbtor_refined0.1690.214731
X-RAY DIFFRACTIONr_nbtor_other0.1270.213175
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.21880
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0420.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1170.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.292
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.2150
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.273
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0130.21
X-RAY DIFFRACTIONr_mcbond_it0.4251.518811
X-RAY DIFFRACTIONr_mcbond_other01.57590
X-RAY DIFFRACTIONr_mcangle_it0.778230174
X-RAY DIFFRACTIONr_scbond_it0.779311189
X-RAY DIFFRACTIONr_scangle_it1.3534.510567
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 174 -
Rwork0.317 14156 -
obs-14330 95.6 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2916-1.95090.37263.6828-0.51432.33440.17210.2019-0.2461-0.5382-0.1210.31970.10110.0515-0.0511-0.10820.0387-0.0053-0.18360.0492-0.2231-38.2227-25.910615.6214
22.85570.40350.57473.3368-1.02571.0943-0.0939-0.1834-0.23780.0237-0.2678-0.63150.03660.44060.3617-0.31560.05350.0057-0.07020.178-0.1759-20.1399-21.964423.634
32.6376-0.7806-0.0352.8283-0.64850.6969-0.0045-0.31970.09550.3605-0.2712-0.3079-0.42220.42540.2757-0.0896-0.0387-0.1272-0.01010.0608-0.1158-23.2823-7.789124.0125
46.9732-2.8859-2.56645.47481.99186.09380.1078-0.00790.2560.0395-0.1254-0.042-0.27840.11280.0175-0.0073-0.02210.0129-0.10010.0017-0.1099-35.78554.550214.7875
56.2957-0.25991.528425.135417.887719.86180.0992-0.84081.05260.74410.2063-1.0458-0.55180.0439-0.30540.1435-0.0879-0.06710.08230.00250.1825-28.66698.991819.432
66.53761.9738-1.80522.9372-0.72781.3162-0.2408-0.1354-1.3631-0.02690.0539-0.40370.208-0.04560.18690.1362-0.1049-0.0433-0.16810.00740.1747-9.6-71.737953.3944
74.47450.2641-0.60462.8036-0.68731.4116-0.33020.782-0.8567-0.49030.49060.37220.5918-0.5523-0.16040.0137-0.3232-0.16320.06330.0373-0.0156-28.1575-67.524546.6485
85.56551.64240.06162.2826-0.67741.0222-0.05290.69590.0986-0.29070.43750.22960.2851-0.5877-0.3846-0.0323-0.1753-0.11820.15640.2013-0.116-25.018-53.348946.6
94.67352.5979-1.75384.5219-1.86144.85510.08710.10870.18350.08640.08740.15520.0866-0.2469-0.1745-0.05020.00220.0219-0.06950.0491-0.0925-11.9714-41.32555.4415
105.1497-1.2391.961725.509-18.712821.07760.02120.70980.85450.00810.4530.747-0.515-0.7679-0.4741-0.05840.02180.0230.13330.15380.0829-19.4166-37.055351.1843
112.93411.688-0.23534.1901-0.45872.14010.1203-0.21070.27910.5318-0.0990.2983-0.05010.1237-0.0212-0.1237-0.03720.0512-0.17210.0333-0.19677.2463-21.323753.7743
122.7616-0.4904-0.64423.3699-0.91811.1622-0.09320.17210.2683-0.0412-0.2694-0.6599-0.03530.47310.3626-0.3186-0.0420.041-0.04590.1928-0.160525.3525-25.261545.7948
133.20550.56190.41163.2921-1.13190.7518-0.04810.2834-0.1318-0.3694-0.2949-0.40610.36330.34920.3429-0.08550.05560.18380.01260.0748-0.114422.0645-39.777145.4762
147.19973.22332.92085.2192.0866.0720.1531-0.0165-0.22030.029-0.1902-0.03960.33310.14490.0371-0.01090.04250.0386-0.08260.0061-0.09789.6364-51.774854.6051
157.072-1.859-1.765127.17318.231320.11050.09750.8705-1.2292-0.65980.2376-0.58230.68220.3892-0.3350.11510.09820.070.0876-0.02150.218916.7286-56.253650.051
1611.82285.1218-0.0596.8102-1.67550.59320.0502-1.27791.90810.1691-0.51180.0219-0.4740.72730.46160.1964-0.1079-0.03120.1563-0.02680.453735.4689-59.321113.0084
1711.9214-1.65030.79152.4784-0.71141.5452-0.1856-0.09230.9030.04560.1911-0.0748-0.2253-0.2388-0.00550.10890.12540.0794-0.1542-0.0447-0.04735.8579-74.98418.8999
184.6243-0.38070.50142.7948-0.83561.397-0.3948-0.76090.85830.55090.51640.399-0.669-0.4529-0.12160.03820.28610.15490.12230.0641-0.018417.3977-71.646222.7059
195.1644-1.61150.36912.9314-0.23710.8683-0.1055-0.6689-0.13020.29210.45280.3135-0.2504-0.5792-0.3473-0.06410.17210.18780.19230.2059-0.123920.6722-86.163622.6881
205.4549-2.70362.35694.7163-2.04585.54210.0933-0.0494-0.0947-0.06190.0940.1542-0.0291-0.2747-0.1873-0.0458-0.00580.0193-0.0790.0609-0.085533.6194-97.85613.9435
216.63681.2061-1.486121.709-16.417419.89770.1127-0.9472-0.95990.03140.53110.92410.6322-0.5165-0.6439-0.0340.00580.0180.15980.19470.09526.08-102.116318.1504
223.45821.73380.39373.71340.34252.05930.1442-0.1626-0.26270.5483-0.1353-0.29370.0562-0.0852-0.0088-0.1066-0.0458-0.0071-0.1907-0.0309-0.209437.0236-25.9217-16.4488
232.7644-0.33250.60933.51031.00731.2774-0.08650.2061-0.2236-0.0293-0.28150.66590.0664-0.48560.368-0.3223-0.06110.0023-0.075-0.171-0.170818.952-21.9812-24.4595
242.0310.5273-0.1753.02851.03480.63560.00560.35010.095-0.3956-0.32320.4273-0.4146-0.42280.3176-0.09060.0474-0.12450.0032-0.0535-0.082622.096-7.8093-24.85
256.85012.7739-2.67655.4429-2.23266.22240.1121-0.07160.2362-0.021-0.13720.0928-0.3013-0.08660.0251-0.01070.01830.0069-0.0980.0092-0.103434.59754.5287-15.6263
267.1631-0.7211.024731.2542-21.598220.87250.25170.73371.2484-0.88330.04310.9022-0.1014-0.261-0.29480.06910.1051-0.03160.05490.02610.117427.55478.2866-19.4704
273.0816-2.0218-0.2914.93620.36242.02430.11610.1910.3025-0.5577-0.138-0.2901-0.0604-0.06720.0219-0.11990.02860.0446-0.1571-0.0223-0.201-8.8894-21.319285.8194
282.8830.3805-0.4953.34310.97811.1722-0.1297-0.25440.30010.001-0.26820.6643-0.0372-0.46870.3979-0.31090.0470.0272-0.0514-0.1795-0.1586-26.989-25.255993.8122
292.4517-0.36920.15793.68521.43471.4462-0.0067-0.4531-0.06940.2789-0.32180.42520.3832-0.39250.3285-0.0984-0.05760.16930.0282-0.0525-0.1019-23.7118-39.766694.1391
307.1581-3.12182.80755.2074-1.84986.24250.1820.0715-0.230.0368-0.1790.09630.3263-0.0739-0.0030.0136-0.03740.027-0.09930.0137-0.1049-11.2931-51.767885.0078
317.9596-1.53060.57922.2294-16.805320.60020.276-0.9763-1.21020.27440.42721.25690.7906-0.4074-0.70320.0724-0.0830.04010.09180.02240.1478-18.5612-55.436288.7733
326.28982.32152.0772.99870.82131.0551-0.3465-0.18091.3422-0.10520.09080.4048-0.19420.02850.25570.1193-0.11060.0426-0.1658-0.02050.1721-37.2052-67.4765-16.7994
335.03430.14510.77962.73830.65391.2393-0.3960.76230.9036-0.48610.5458-0.4068-0.57750.5879-0.14980.0036-0.34140.18190.0818-0.0439-0.0202-18.6482-71.6957-23.5127
345.14851.01810.06843.0963-0.1180.8994-0.10110.7046-0.1067-0.34360.4782-0.3967-0.26390.6008-0.3771-0.0403-0.18620.18020.1911-0.1905-0.1056-21.804-85.8727-23.5722
355.63833.0412.99244.67251.84125.90250.13660.045-0.09850.09680.0332-0.13750.0290.3264-0.1698-0.07340.01760.0277-0.0617-0.0445-0.0757-34.8797-97.8859-14.7712
365.7703-2.2572-1.944716.664612.095817.02020.09450.5778-0.7170.03740.4424-0.55990.69570.7775-0.5369-0.04530.01360.02050.1731-0.13790.0858-27.5552-101.2934-18.3342
378.37292.4729-2.98764.07160.23391.439-0.391-0.0279-1.837-0.1371-0.1950.04590.4521-0.40740.5860.20520.0172-0.0215-0.0297-0.11040.48348.4218-79.843983.2563
3811.5134-2.7829-0.09482.4010.60161.0568-0.105-0.0371-0.72120.02750.18420.10380.21210.154-0.07920.12490.1045-0.0451-0.14810.0678-0.06318.0453-64.180389.1426
394.3962-0.3564-0.51292.69810.85621.5483-0.377-0.7812-0.81850.54710.4974-0.36250.65020.4509-0.12050.04690.2894-0.15510.1049-0.0422-0.024426.4874-67.524292.9546
404.8335-1.1012-0.49682.95720.77640.5512-0.103-0.65990.05250.45610.4469-0.40730.23240.5874-0.344-0.02610.1865-0.15270.1968-0.1836-0.093123.3574-53.338493.0103
415.4683-2.9112-2.5865.62262.36766.0230.1158-0.06460.1649-0.10430.1035-0.1760.08220.2831-0.2194-0.0771-0.01410.0195-0.0513-0.029-0.107210.3195-41.310884.1695
425.4609-0.1051.22324.985320.104522.419-0.2119-0.62870.9606-0.03041.0041-1.0757-0.57491.0645-0.79230.0043-0.0150.00110.147-0.14180.141717.8477-37.126588.4651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 793 - 79
2X-RAY DIFFRACTION1AI4821
3X-RAY DIFFRACTION2AA80 - 32080 - 320
4X-RAY DIFFRACTION3AA321 - 370321 - 370
5X-RAY DIFFRACTION4AA371 - 449371 - 449
6X-RAY DIFFRACTION5AA450 - 473450 - 473
7X-RAY DIFFRACTION6BB3 - 793 - 79
8X-RAY DIFFRACTION6BJ4821
9X-RAY DIFFRACTION7BB80 - 32080 - 320
10X-RAY DIFFRACTION8BB321 - 370321 - 370
11X-RAY DIFFRACTION9BB371 - 449371 - 449
12X-RAY DIFFRACTION10BB450 - 473450 - 473
13X-RAY DIFFRACTION11CC3 - 793 - 79
14X-RAY DIFFRACTION11CK4821
15X-RAY DIFFRACTION12CC80 - 32180 - 321
16X-RAY DIFFRACTION13CC322 - 370322 - 370
17X-RAY DIFFRACTION14CC371 - 449371 - 449
18X-RAY DIFFRACTION15CC450 - 473450 - 473
19X-RAY DIFFRACTION16DD5 - 415 - 41
20X-RAY DIFFRACTION17DD42 - 7942 - 79
21X-RAY DIFFRACTION17DL4821
22X-RAY DIFFRACTION18DD80 - 32180 - 321
23X-RAY DIFFRACTION19DD322 - 370322 - 370
24X-RAY DIFFRACTION20DD371 - 449371 - 449
25X-RAY DIFFRACTION21DD450 - 473450 - 473
26X-RAY DIFFRACTION22EE3 - 793 - 79
27X-RAY DIFFRACTION22EM4821
28X-RAY DIFFRACTION23EE80 - 32080 - 320
29X-RAY DIFFRACTION24EE321 - 370321 - 370
30X-RAY DIFFRACTION25EE371 - 449371 - 449
31X-RAY DIFFRACTION26EE450 - 474450 - 474
32X-RAY DIFFRACTION27FF3 - 793 - 79
33X-RAY DIFFRACTION27FN4821
34X-RAY DIFFRACTION28FF80 - 32180 - 321
35X-RAY DIFFRACTION29FF322 - 370322 - 370
36X-RAY DIFFRACTION30FF371 - 449371 - 449
37X-RAY DIFFRACTION31FF450 - 474450 - 474
38X-RAY DIFFRACTION32GG3 - 793 - 79
39X-RAY DIFFRACTION32GO4821
40X-RAY DIFFRACTION33GG80 - 32080 - 320
41X-RAY DIFFRACTION34GG321 - 370321 - 370
42X-RAY DIFFRACTION35GG371 - 449371 - 449
43X-RAY DIFFRACTION36GG450 - 474450 - 474
44X-RAY DIFFRACTION37HH5 - 415 - 41
45X-RAY DIFFRACTION38HH42 - 7942 - 79
46X-RAY DIFFRACTION38HP4821
47X-RAY DIFFRACTION39HH80 - 32080 - 320
48X-RAY DIFFRACTION40HH321 - 370321 - 370
49X-RAY DIFFRACTION41HH371 - 449371 - 449
50X-RAY DIFFRACTION42HH450 - 473450 - 473

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