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- PDB-2w9l: CANINE ADENOVIRUS TYPE 2 FIBRE HEAD IN COMPLEX WITH CAR DOMAIN D1... -

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Basic information

Entry
Database: PDB / ID: 2w9l
TitleCANINE ADENOVIRUS TYPE 2 FIBRE HEAD IN COMPLEX WITH CAR DOMAIN D1 AND SIALIC ACID
Components
  • COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
  • FIBRE PROTEIN
KeywordsRECEPTOR / IMMUNOGLOBULIN DOMAIN / CAR / KNOB / FIBER / FIBRE / CAV-2 / CANINE / COMPLEX / ERYTHROCYTE / SIALIC ACID / GLYCOPROTEIN / FIBER HEAD / ADENOVIRUS / FIBRE HEAD / LIPOPROTEIN / FIBER PROTEIN / CELL JUNCTION / CELL ADHESION / RED BLOOD CELL / COXSACKIEVIRUS / PHOSPHOPROTEIN / MEMBRANE / SECRETED / PALMITATE / DOMAIN D1 / HOST-VIRUS INTERACTION / VIRUS-RECEPTOR COMPLEX / TRANSMEMBRANE / CELL MEMBRANE / SIALYL-LACTOSE / TIGHT JUNCTION / PHOSPHORYLATION / HEMAGGLUTINATION
Function / homology
Function and homology information


AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / connexin binding ...AV node cell-bundle of His cell adhesion involved in cell communication / cell adhesive protein binding involved in AV node cell-bundle of His cell communication / AV node cell to bundle of His cell communication / homotypic cell-cell adhesion / epithelial structure maintenance / regulation of AV node cell action potential / gamma-delta T cell activation / apicolateral plasma membrane / germ cell migration / connexin binding / transepithelial transport / cell-cell junction organization / adhesion receptor-mediated virion attachment to host cell / cardiac muscle cell development / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / intercalated disc / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / acrosomal vesicle / Cell surface interactions at the vascular wall / adherens junction / mitochondrion organization / filopodium / PDZ domain binding / neuromuscular junction / beta-catenin binding / integrin binding / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / cell junction / viral capsid / heart development / growth cone / cell body / virus receptor activity / actin cytoskeleton organization / basolateral plasma membrane / defense response to virus / neuron projection / cell adhesion / membrane raft / signaling receptor binding / symbiont entry into host cell / host cell nucleus / protein-containing complex / extracellular space / extracellular region / nucleoplasm / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain ...: / Adenovirus pIV-related, attachment domain / Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) / Adenoviral fibre protein, repeat/shaft region / Adenoviral fibre protein, knob / Adenoviral fibre protein (knob domain) / Adenoviral fibre protein (repeat/shaft region) / Adenovirus fibre protein / Attachment protein shaft domain superfamily / Adenovirus pIV-like, attachment domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coxsackievirus and adenovirus receptor / Fiber protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
CANINE ADENOVIRUS 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsSeiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. ...Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / Finberg, R.W. / Cusack, S. / Kremer, E.J.
CitationJournal: PLoS Pathog. / Year: 2009
Title: The cell adhesion molecule "CAR" and sialic acid on human erythrocytes influence adenovirus in vivo biodistribution.
Authors: Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / ...Authors: Seiradake, E. / Henaff, D. / Wodrich, H. / Billet, O. / Perreau, M. / Hippert, C. / Mennechet, F. / Schoehn, G. / Lortat-Jacob, H. / Dreja, H. / Ibanes, S. / Kalatzis, V. / Wang, J.P. / Finberg, R.W. / Cusack, S. / Kremer, E.J.
History
DepositionJan 26, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 17, 2011Group: Atomic model / Derived calculations / Other
Revision 1.3Jul 12, 2017Group: Advisory / Category: database_PDB_caveat
Revision 2.0Jan 23, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / database_PDB_caveat / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _database_PDB_caveat.text / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.details / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 4.0Jul 21, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
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 / _chem_comp.pdbx_synonyms / _pdbx_nonpoly_scheme.auth_seq_num / _struct_conn.pdbx_value_order
Revision 4.1Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 4.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
B: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
C: FIBRE PROTEIN
D: FIBRE PROTEIN
E: FIBRE PROTEIN
F: FIBRE PROTEIN
G: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
H: FIBRE PROTEIN
I: FIBRE PROTEIN
J: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
K: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
L: FIBRE PROTEIN
M: FIBRE PROTEIN
N: FIBRE PROTEIN
O: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
P: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
Q: FIBRE PROTEIN
R: FIBRE PROTEIN
S: FIBRE PROTEIN
T: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
V: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
X: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
Y: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
Z: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,54036
Polymers425,88324
Non-polymers5,65712
Water2,828157
1
A: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
G: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
Q: FIBRE PROTEIN
R: FIBRE PROTEIN
S: FIBRE PROTEIN
Z: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8859
Polymers106,4716
Non-polymers1,4143
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
D: FIBRE PROTEIN
E: FIBRE PROTEIN
F: FIBRE PROTEIN
K: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
O: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8859
Polymers106,4716
Non-polymers1,4143
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FIBRE PROTEIN
H: FIBRE PROTEIN
I: FIBRE PROTEIN
J: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
P: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
T: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8859
Polymers106,4716
Non-polymers1,4143
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
L: FIBRE PROTEIN
M: FIBRE PROTEIN
N: FIBRE PROTEIN
V: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
X: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
Y: COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,8859
Polymers106,4716
Non-polymers1,4143
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)221.150, 221.150, 391.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11J
21T
31O
41K
51P
61V
71X
81Y
91A
101G
111Z
12H
22C
32D
42E
52F
62I
72L
82M
92N
102Q
112R
122S

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115J19 - 80
2115T19 - 80
3115O19 - 80
4115K19 - 80
5115P19 - 80
6115V19 - 80
7115X19 - 80
8115Y19 - 80
9115A19 - 80
10115G19 - 80
11115Z19 - 80
1215J83 - 137
2215T83 - 137
3215O83 - 137
4215K83 - 137
5215P83 - 137
6215V83 - 137
7215X83 - 137
8215Y83 - 137
9215A83 - 137
10215G83 - 137
11215Z83 - 137
1122H361 - 373
2122C361 - 373
3122D361 - 373
4122E361 - 373
5122F361 - 373
6122I361 - 373
7122L361 - 373
8122M361 - 373
9122N361 - 373
10122Q361 - 373
11122R361 - 373
12122S361 - 373
1222H383 - 542
2222C383 - 542
3222D383 - 542
4222E383 - 542
5222F383 - 542
6222I383 - 542
7222L383 - 542
8222M383 - 542
9222N383 - 542
10222Q383 - 542
11222R383 - 542
12222S383 - 542

NCS ensembles :
ID
1
2

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Components

#1: Protein
COXSACKIEVIRUS AND ADENOVIRUS RECEPTOR / COXSACKIEVIRUS B-ADENOVIRUS RECEPTOR / HCVADR / HCAR / CVB3-BINDING PROTEIN


Mass: 13804.705 Da / Num. of mol.: 12 / Fragment: DOMAIN D1, RESIDUES 16-139
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): XL1 BLUE / References: UniProt: P78310
#2: Protein
FIBRE PROTEIN / CANINE ADENOVIRUS FIBRE HEAD / PIV


Mass: 21685.541 Da / Num. of mol.: 12 / Fragment: FIBRE HEAD, RESIDUES 358-542
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CANINE ADENOVIRUS 2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): Star / References: UniProt: Q65914
#3: Polysaccharide
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Gulp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-gulopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGulpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2212h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][b-D-Gulp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCONTAINS POLY-HIS TAG

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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: 2.9 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growDetails: 20% POLYETHYLENE GLYCOL MONOMETHYL-ETHER 550, 0.1 M BICINE, PH 9, 0.1 M NACL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.9→49.6 Å / Num. obs: 105112 / % possible obs: 98.3 % / Observed criterion σ(I): 1 / Redundancy: 8.18 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.18
Reflection shellResolution: 2.9→3 Å / Redundancy: 8.37 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.3 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J1K

2j1k


Resolution: 2.91→49.63 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.893 / SU B: 34.734 / SU ML: 0.299 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE 24 NCS OPERATIONS, WHICH CAN BE PICKED UP EASILY WITH REGULAR CRYSTALLOGRAPHIC SOFTWARE.
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1034 1 %RANDOM
Rwork0.197 ---
obs0.197 104076 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.92 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å20 Å20 Å2
2---1.54 Å20 Å2
3---3.09 Å2
Refinement stepCycle: LAST / Resolution: 2.91→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28130 0 384 157 28671
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02229219
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219515
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.97739835
X-RAY DIFFRACTIONr_angle_other_deg0.9773.00147947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69953608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.57624.7491194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.872154783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.28715127
X-RAY DIFFRACTIONr_chiral_restr0.1490.24626
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0231926
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025525
X-RAY DIFFRACTIONr_nbd_refined0.1940.24957
X-RAY DIFFRACTIONr_nbd_other0.190.219518
X-RAY DIFFRACTIONr_nbtor_refined0.1770.214300
X-RAY DIFFRACTIONr_nbtor_other0.0850.215559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1240.2501
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1940.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3051.523402
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.391229548
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.823313015
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4484.510287
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
21H1011tight positional0.030.05
22C1011tight positional0.030.05
23D1011tight positional0.030.05
24E1011tight positional0.030.05
25F1011tight positional0.030.05
26I1011tight positional0.030.05
27L1011tight positional0.030.05
28M1011tight positional0.030.05
29N1011tight positional0.030.05
210Q1011tight positional0.030.05
211R1011tight positional0.030.05
212S1011tight positional0.030.05
11J657medium positional0.230.5
12T657medium positional0.230.5
13O657medium positional0.30.5
14K657medium positional0.230.5
15P657medium positional0.250.5
16V657medium positional0.260.5
17X657medium positional0.220.5
18Y657medium positional0.180.5
19A657medium positional0.230.5
110G657medium positional0.240.5
111Z657medium positional0.270.5
21H1250medium positional0.280.5
22C1250medium positional0.260.5
23D1250medium positional0.30.5
24E1250medium positional0.360.5
25F1250medium positional0.230.5
26I1250medium positional0.290.5
27L1250medium positional0.290.5
28M1250medium positional0.420.5
29N1250medium positional0.410.5
210Q1250medium positional0.250.5
211R1250medium positional0.250.5
212S1250medium positional0.280.5
11J815loose positional0.715
12T815loose positional0.735
13O815loose positional0.755
14K815loose positional0.715
15P815loose positional0.675
16V815loose positional0.745
17X815loose positional0.735
18Y815loose positional0.665
19A815loose positional0.815
110G815loose positional0.725
111Z815loose positional0.865
21H1011tight thermal0.050.5
22C1011tight thermal0.050.5
23D1011tight thermal0.050.5
24E1011tight thermal0.050.5
25F1011tight thermal0.050.5
26I1011tight thermal0.050.5
27L1011tight thermal0.040.5
28M1011tight thermal0.050.5
29N1011tight thermal0.050.5
210Q1011tight thermal0.040.5
211R1011tight thermal0.050.5
212S1011tight thermal0.040.5
11J657medium thermal0.232
12T657medium thermal0.272
13O657medium thermal0.22
14K657medium thermal0.262
15P657medium thermal0.222
16V657medium thermal0.212
17X657medium thermal0.272
18Y657medium thermal0.252
19A657medium thermal0.22
110G657medium thermal0.292
111Z657medium thermal0.212
21H1250medium thermal0.32
22C1250medium thermal0.282
23D1250medium thermal0.282
24E1250medium thermal0.282
25F1250medium thermal0.292
26I1250medium thermal0.282
27L1250medium thermal0.292
28M1250medium thermal0.312
29N1250medium thermal0.312
210Q1250medium thermal0.272
211R1250medium thermal0.272
212S1250medium thermal0.272
11J815loose thermal0.7210
12T815loose thermal0.7110
13O815loose thermal0.5110
14K815loose thermal0.7110
15P815loose thermal0.610
16V815loose thermal0.610
17X815loose thermal0.7510
18Y815loose thermal0.7210
19A815loose thermal0.6510
110G815loose thermal0.8210
111Z815loose thermal0.5710
LS refinement shellResolution: 2.91→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 79 -
Rwork0.292 7640 -
obs--99.69 %
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)
15.96650.02480.89423.1657-0.44112.66020.08780.0542-0.21740.0252-0.1272-0.91510.29360.88070.0394-0.02970.07470.10950.3648-0.01140.3605-48.359722.3372-184.7622
210.63411.429-1.872210.49083.0616.7636-0.74660.763-1.57471.4158-0.19281.01061.7908-1.03860.93930.7637-0.30940.47270.1914-0.17040.212-52.901-33.4086-102.7352
31.48630.5777-0.169211.11140.1542.722-0.00950.33920.1344-0.5818-0.0201-0.0665-0.51150.10330.02960.01940.0420.0627-0.0577-0.018-0.189-103.931258.1964-177.8684
42.94480.2169-0.74971.6935-0.64289.269-0.035-0.7883-0.06930.1278-0.079-0.25440.39370.3870.114-0.184-0.0036-0.04950.0984-0.06040.0504-22.14545.3826-34.4083
53.37660.0671.68621.8942-1.255510.1844-0.12770.5210.2447-0.0743-0.0272-0.1606-0.28590.57410.155-0.1589-0.05040.07230.1233-0.0603-0.0286-19.8279-10.1091-156.1414
66.3505-2.8261-1.21393.25670.45682.659-0.1361-0.33620.58640.0760.13570.2109-0.3055-0.35930.00040.09980.02720.00820.0563-0.05030.1318-50.160232.8929-115.2274
75.5877-3.4549-1.76245.84212.09512.69990.12330.15150.4786-0.3599-0.15650.3867-0.6374-0.34610.03320.31710.0866-0.2106-0.0059-0.00190.0715-59.881420.7092-87.65
86.39654.51090.73156.43091.18463.2517-0.20130.403-0.1569-0.47410.3250.44010.2381-0.2261-0.1237-0.01490.0016-0.0216-0.09020.0203-0.018-42.6421-42.5573-74.6254
92.80610.36930.29729.43341.11663.01240.04590.1161-0.7240.27280.13640.2410.8643-0.1848-0.18220.2034-0.0588-0.06520.0583-0.09430.0774-89.9449-59.0343-189.181
107.6292-0.9886-0.49862.63180.23283.00570.10410.63870.1475-0.3002-0.06130.18070.01320.5785-0.0429-0.0436-0.1127-0.00990.06650.0223-0.1647-48.6992-9.8491-174.3253
112.30541.16840.96083.48570.16019.06590.021-0.46020.1140.65870.0404-0.0126-0.4255-0.0229-0.0614-0.0347-0.0480.0576-0.02840.0126-0.0286-103.3255-20.1797-136.6712
124.02991.285-1.04843.35190.51978.58590.1166-0.67310.01320.9021-0.25420.2722-0.2978-0.38570.13760.1611-0.01090.03380.04120.09440.0924-90.33737.608-135.8464
130.92080.31330.41931.9760.18462.00340.0259-0.184-0.10320.01320.00040.05830.1421-0.0052-0.0263-0.2388-0.00230.0515-0.1922-0.0179-0.1965-38.8666-19.3143-61.5284
140.64620.0245-0.25412.22770.24841.80460.0078-0.08250.07090.2784-0.22150.35380.143-0.45640.2137-0.1619-0.09050.0631-0.0408-0.077-0.156-50.3115-8.8096-113.5386
150.970.3346-0.4441.80880.0972.628-0.01910.15960.1879-0.1215-0.01010.1997-0.4231-0.2110.0292-0.16240.0216-0.0302-0.1506-0.02-0.1759-42.13410.3822-129.1922
161.48680.3043-0.08561.82430.17242.14460.01880.0738-0.1049-0.0731-0.05640.04020.19880.06080.0377-0.2725-0.0262-0.0036-0.1458-0.0336-0.2046-36.2286-14.3485-134.7995
171.6747-0.2241-0.00521.7218-0.27761.593-0.0606-0.06980.17660.12940.03980.0034-0.1622-0.04940.0208-0.2651-0.0032-0.013-0.1666-0.0811-0.1888-38.5516.1244-55.9969
181.6129-0.29280.04462.05350.55971.2347-0.05830.0209-0.1026-0.3632-0.08210.3712-0.0536-0.17840.1404-0.1591-0.0105-0.0653-0.1346-0.0374-0.1661-51.1521-2.4894-77.1305
192.16890.13950.02631.4665-0.2831.05130.0230.2255-0.2748-0.1016-0.0411-0.11230.14520.15490.018-0.18810.028-0.0524-0.1889-0.0483-0.1147-76.3272-38.999-177.338
201.9984-0.18670.2811.00020.00851.77330.024-0.01040.0820.05960.0044-0.0812-0.05490.0979-0.0284-0.2018-0.0446-0.0232-0.26720.0216-0.1722-70.7964-19.1838-161.3929
211.43370.35580.55461.15760.28791.22580.2084-0.0859-0.16580.0198-0.10670.03770.1498-0.1411-0.1017-0.2203-0.0166-0.0193-0.23380.0426-0.1169-92.4661-33.2441-157.6822
221.9964-0.03840.33042.197-0.29341.3249-0.00020.09150.0518-0.1089-0.0898-0.2555-0.13520.18620.0901-0.2284-0.02010.0476-0.1684-0.0206-0.1305-70.895934.3465-176.2771
231.3635-0.1149-0.29561.1874-0.40771.93120.0971-0.08650.04560.2018-0.0820.0527-0.1351-0.0094-0.0151-0.2022-0.00250.0097-0.243-0.0206-0.1911-92.917738.2923-162.7998
241.8965-0.1982-0.20721.0681-0.22051.3752-0.0421-0.1827-0.23250.14650.0523-0.19750.03360.1907-0.0102-0.1853-0.0319-0.0169-0.22390.0575-0.054-76.694719.0521-156.0487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A19 - 135
2X-RAY DIFFRACTION2B20 - 136
3X-RAY DIFFRACTION3G17 - 139
4X-RAY DIFFRACTION4J17 - 139
5X-RAY DIFFRACTION5K16 - 138
6X-RAY DIFFRACTION6O19 - 139
7X-RAY DIFFRACTION7P17 - 139
8X-RAY DIFFRACTION8T19 - 137
9X-RAY DIFFRACTION9V17 - 137
10X-RAY DIFFRACTION10X17 - 139
11X-RAY DIFFRACTION11Y19 - 137
12X-RAY DIFFRACTION12Z19 - 135
13X-RAY DIFFRACTION13C361 - 542
14X-RAY DIFFRACTION14D361 - 542
15X-RAY DIFFRACTION15E361 - 542
16X-RAY DIFFRACTION16F361 - 542
17X-RAY DIFFRACTION17H361 - 542
18X-RAY DIFFRACTION18I361 - 542
19X-RAY DIFFRACTION19L361 - 542
20X-RAY DIFFRACTION20M361 - 542
21X-RAY DIFFRACTION21N361 - 542
22X-RAY DIFFRACTION22Q361 - 542
23X-RAY DIFFRACTION23R361 - 542
24X-RAY DIFFRACTION24S361 - 542

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