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- PDB-5osq: ZP-N domain of mammalian sperm receptor ZP3 (crystal form II, pro... -

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Entry
Database: PDB / ID: 5osq
TitleZP-N domain of mammalian sperm receptor ZP3 (crystal form II, processed in P21221)
ComponentsMaltose-binding periplasmic protein,Zona pellucida sperm-binding 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 transport complex / positive regulation of interleukin-4 production / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 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 ...: / 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
Similarity search - Domain/homology
alpha-maltose / TRIETHYLENE GLYCOL / Maltose/maltodextrin-binding periplasmic protein / Zona pellucida sperm-binding protein 3
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsJovine, L. / Monne, M.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research CouncilProject grant 2005-5102 Sweden
European UnionMarie Curie ERG 31055
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.
#7: Journal: Cell / Year: 2010
Title: Insights into egg coat assembly and egg-sperm interaction from the X-ray structure of full-length ZP3.
Authors: Ling Han / Magnus Monné / Hiroki Okumura / Thomas Schwend / Amy L Cherry / David Flot / Tsukasa Matsuda / Luca Jovine /
Abstract: ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization- ...ZP3, a major component of the zona pellucida (ZP) matrix coating mammalian eggs, is essential for fertilization by acting as sperm receptor. By retaining a propeptide that contains a polymerization-blocking external hydrophobic patch (EHP), we determined the crystal structure of an avian homolog of ZP3 at 2.0 Å resolution. The structure unveils the fold of a complete ZP domain module in a homodimeric arrangement required for secretion and reveals how EHP prevents premature incorporation of ZP3 into the ZP. This suggests mechanisms underlying polymerization and how local structural differences, reflected by alternative disulfide patterns, control the specificity of ZP subunit interaction. Close relative positioning of a conserved O-glycan important for sperm binding and the hypervariable, positively selected C-terminal region of ZP3 suggests a concerted role in the regulation of species-restricted gamete recognition. Alternative conformations of the area around the O-glycan indicate how sperm binding could trigger downstream events via intramolecular signaling.
#8: Journal: Biol. Reprod. / Year: 2011
Title: A structural view of egg coat architecture and function in fertilization
Authors: Monne, M. / Jovine, L.
History
DepositionAug 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
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.occupancy / _atom_site.pdbx_formal_charge / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Maltose-binding periplasmic protein,Zona pellucida sperm-binding protein 3
B: Maltose-binding periplasmic protein,Zona pellucida sperm-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,97311
Polymers105,8982
Non-polymers1,0759
Water5,567309
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A: Maltose-binding periplasmic protein,Zona pellucida sperm-binding 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
2
B: Maltose-binding periplasmic protein,Zona pellucida sperm-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5626
Polymers52,9491
Non-polymers6135
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.340, 92.160, 140.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(CHAIN A AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))
21(CHAIN B AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(CHAIN A AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))AA33
12LYSLYSLYSLYS(CHAIN A AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))AA4343
13THRTHRTHRTHR(CHAIN A AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))AA346346
21THRTHRTHRTHR(CHAIN B AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))BB33
22LYSLYSLYSLYS(CHAIN B AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))BB4343
23THRTHRTHRTHR(CHAIN B AND (RESID 3 THROUGH 41 OR RESID 43 THROUGH 344 OR RESID 346 THROUGH 473))BB346346

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Components

#1: Protein Maltose-binding periplasmic protein,Zona pellucida sperm-binding protein 3 / MBP / MMBP / Maltodextrin-binding protein / Sperm receptor / Zona pellucida glycoprotein 3 / Zp-3 / ...MBP / MMBP / Maltodextrin-binding protein / Sperm receptor / Zona pellucida glycoprotein 3 / Zp-3 / Zona pellucida protein C


Mass: 52948.945 Da / Num. of mol.: 2
Fragment: UNP RESIDUES 27-393,ZP3 ZP-N domain, UNP residues 42-143
Mutation: I28T, E385A, K388A, D389A, R393N
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 K-12 (bacteria), (gene. exp.) Mus musculus (house mouse)
Cellular location: EXTRACELLULAR MATRIX / Gene: malE, b4034, JW3994, Zp3, Zp-3, Zpc / Plasmid: PLJMBP4C, PLJDIS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B / 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.: 2
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.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 309 / 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: 2.8 Å3/Da / Density % sol: 56.17 %
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
PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535 Å
DetectorType: MARRESEARCH / 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: 2.05→50 Å / Num. obs: 75254 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.43 % / CC1/2: 0.999 / Rsym value: 0.106 / Net I/σ(I): 13.09
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 7.51 % / Mean I/σ(I) obs: 0.67 / Num. unique obs: 5501 / CC1/2: 0.188 / Rsym value: 0.3863 / % possible all: 99.9

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Processing

Software
NameVersionClassification
XDSJun 1, 2017 BUILT=20170720data reduction
XDSJun 1, 2017 BUILT=20170720data scaling
PHASER2.6.0phasing
PHENIX1.12-2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D4C

3d4c


Resolution: 2.05→32.898 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.84
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 1857 2.47 %RANDOM
Rwork0.2091 ---
obs0.2099 75143 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 66 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7291 0 62 309 7662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117580
X-RAY DIFFRACTIONf_angle_d0.78310266
X-RAY DIFFRACTIONf_dihedral_angle_d12.5532795
X-RAY DIFFRACTIONf_chiral_restr0.0461152
X-RAY DIFFRACTIONf_plane_restr0.0061327
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5614X-RAY DIFFRACTION5.185TORSIONAL
12B5614X-RAY DIFFRACTION5.185TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.12330.38081800.36537210X-RAY DIFFRACTION100
2.1233-2.20830.36271810.34997250X-RAY DIFFRACTION100
2.2083-2.30870.37871870.33187261X-RAY DIFFRACTION100
2.3087-2.43040.31111800.2897266X-RAY DIFFRACTION100
2.4304-2.58260.2971860.26657265X-RAY DIFFRACTION100
2.5826-2.78190.25741840.25387303X-RAY DIFFRACTION100
2.7819-3.06170.27911910.23857335X-RAY DIFFRACTION100
3.0617-3.50430.24921870.21627353X-RAY DIFFRACTION100
3.5043-4.41340.20181860.16287418X-RAY DIFFRACTION100
4.4134-32.90240.18811950.16077625X-RAY DIFFRACTION99
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)
13.16510.63910.95581.43890.25510.8479-0.33680.5470.6031-0.29280.4286-0.1648-0.38350.48130.01890.595-0.24240.09540.5401-0.00980.4903114.30889.001148.8151
20.94470.2452-0.18160.43580.0550.38460.06630.0577-0.13950.11970.0523-0.04610.00840.0359-00.4673-0.0032-0.030.4618-0.08320.426104.441562.953155.1983
32.0187-0.1042-0.08832.46341.10431.3493-0.0841-0.16290.216-0.0794-0.19470.3039-0.0599-0.3228-0.07620.32070.0448-0.00450.4338-0.09910.3355115.331143.297522.3083
40.8995-0.2313-0.34270.50630.07660.40110.10520.0376-0.1603-0.0767-0.1222-0.00980.2210.007500.5076-0.0328-0.01810.39360.0350.3931124.852116.689716.2748
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESI 3:371 OR RESI 900)
2X-RAY DIFFRACTION2CHAIN A AND RESI 372:474
3X-RAY DIFFRACTION3CHAIN B AND (RESI 2:371 OR RESI 900)
4X-RAY DIFFRACTION4CHAIN B AND RESI 372:473

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