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- PDB-3ghg: Crystal Structure of Human Fibrinogen -

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Basic information

Entry
Database: PDB / ID: 3ghg
TitleCrystal Structure of Human Fibrinogen
Components
  • A knob
  • B knob
  • Fibrinogen alpha chain
  • Fibrinogen beta chain
  • Fibrinogen gamma chain
KeywordsBLOOD CLOTTING / triple-stranded coiled coil / beta sheets / alpha helices / Amyloid / Amyloidosis / Blood coagulation / Disease mutation / Glycoprotein / Phosphoprotein / Secreted / Pyrrolidone carboxylic acid / Sulfation
Function / homology
Function and homology information


platelet maturation / induction of bacterial agglutination / blood coagulation, common pathway / sugar-phosphatase activity / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to interleukin-6 / positive regulation of heterotypic cell-cell adhesion ...platelet maturation / induction of bacterial agglutination / blood coagulation, common pathway / sugar-phosphatase activity / fibrinogen complex / Regulation of TLR by endogenous ligand / platelet alpha granule / blood coagulation, fibrin clot formation / cellular response to interleukin-6 / positive regulation of heterotypic cell-cell adhesion / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / extracellular matrix structural constituent / plasminogen activation / p130Cas linkage to MAPK signaling for integrins / positive regulation of peptide hormone secretion / positive regulation of exocytosis / GRB2:SOS provides linkage to MAPK signaling for Integrins / cellular response to interleukin-1 / protein polymerization / protein secretion / Integrin cell surface interactions / negative regulation of endothelial cell apoptotic process / Common Pathway of Fibrin Clot Formation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of substrate adhesion-dependent cell spreading / cell adhesion molecule binding / positive regulation of vasoconstriction / fibrinolysis / Integrin signaling / cell-matrix adhesion / platelet alpha granule lumen / positive regulation of protein secretion / Post-translational protein phosphorylation / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / platelet aggregation / response to calcium ion / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / extracellular vesicle / Platelet degranulation / protein-macromolecule adaptor activity / outer membrane-bounded periplasmic space / ER-Phagosome pathway / protein-containing complex assembly / collagen-containing extracellular matrix / blood microparticle / adaptive immune response / positive regulation of ERK1 and ERK2 cascade / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / innate immune response / signaling receptor binding / structural molecule activity / cell surface / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / metal ion binding / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #50 / Fibrinogen alpha C domain / Fibrinogen alpha C domain / Fibrinogen, alpha/beta/gamma chain, coiled coil domain / Fibrinogen alpha/beta chain family / Fibrinogen alpha/beta chain family / Fibrinogen alpha chain / Gamma-fibrinogen Carboxyl Terminal Fragment; domain 2 / Gamma-fibrinogen Carboxyl Terminal Fragment, domain 2 / Gamma Fibrinogen; Chain A, domain 1 / Gamma Fibrinogen, chain A, domain 1 / Histidine acid phosphatases active site signature. / : / Fibrinogen, conserved site / Fibrinogen C-terminal domain signature. / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Fibrinogen-related domains (FReDs) / Fibrinogen beta and gamma chains, C-terminal globular domain / Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 / Fibrinogen, alpha/beta/gamma chain, C-terminal globular domain / Fibrinogen-like, C-terminal / Fibrinogen C-terminal domain profile. / Histidine phosphatase superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Few Secondary Structures / Irregular / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Fibrinogen alpha chain / Acid glucose-1-phosphate phosphatase / Fibrinogen gamma chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsDoolittle, R.F. / Kollman, J.M. / Sawaya, M.R. / Pandi, L. / Riley, M.
CitationJournal: Biochemistry / Year: 2009
Title: Crystal structure of human fibrinogen.
Authors: Kollman, J.M. / Pandi, L. / Sawaya, M.R. / Riley, M. / Doolittle, R.F.
History
DepositionMar 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0May 3, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / database_PDB_caveat / entity / entity_name_com / entity_src_nat / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_src_syn / pdbx_validate_chiral / struct_conn / struct_ncs_dom_lim / struct_ref / struct_ref_seq / struct_ref_seq_dif
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.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entity_branch_link.comp_id_1 / _pdbx_entity_branch_link.comp_id_2 / _pdbx_entity_branch_list.comp_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _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: Fibrinogen alpha chain
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
D: Fibrinogen alpha chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
G: Fibrinogen alpha chain
H: Fibrinogen beta chain
I: Fibrinogen gamma chain
J: Fibrinogen alpha chain
K: Fibrinogen beta chain
L: Fibrinogen gamma chain
M: A knob
N: A knob
O: B knob
P: B knob
Q: A knob
R: A knob
S: B knob
T: B knob
hetero molecules


Theoretical massNumber of molelcules
Total (without water)651,38833
Polymers643,06020
Non-polymers8,32813
Water00
1
A: Fibrinogen alpha chain
B: Fibrinogen beta chain
C: Fibrinogen gamma chain
D: Fibrinogen alpha chain
E: Fibrinogen beta chain
F: Fibrinogen gamma chain
M: A knob
N: A knob
O: B knob
P: B knob
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,13816
Polymers321,53010
Non-polymers4,6086
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Fibrinogen alpha chain
H: Fibrinogen beta chain
I: Fibrinogen gamma chain
J: Fibrinogen alpha chain
K: Fibrinogen beta chain
L: Fibrinogen gamma chain
Q: A knob
R: A knob
S: B knob
T: B knob
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,24917
Polymers321,53010
Non-polymers3,7207
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.238, 94.866, 300.812
Angle α, β, γ (deg.)90.00, 94.81, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21E
31H
41K

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 5 / Auth seq-ID: 202 - 458 / Label seq-ID: 202 - 458

Dom-IDAuth asym-IDLabel asym-ID
1BB
2EE
3HH
4KK

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Components

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Protein , 3 types, 12 molecules ADGJBEHKCFIL

#1: Protein
Fibrinogen alpha chain


Mass: 60969.754 Da / Num. of mol.: 4 / Fragment: mature chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood plasma / References: UniProt: P02671
#2: Protein
Fibrinogen beta chain


Mass: 52379.438 Da / Num. of mol.: 4 / Fragment: mature chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood plasma / References: UniProt: P02675
#3: Protein
Fibrinogen gamma chain


Mass: 46521.777 Da / Num. of mol.: 4 / Fragment: mature chain / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood plasma / References: UniProt: P02679

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Protein/peptide , 2 types, 8 molecules MNQROPST

#4: Protein/peptide
A knob


Mass: 426.490 Da / Num. of mol.: 4 / Source method: obtained synthetically
#5: Protein/peptide
B knob


Mass: 467.522 Da / Num. of mol.: 4 / Source method: obtained synthetically

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Sugars , 3 types, 5 molecules

#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2224.000 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-3[DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-3-1-4-5-3-1-4-5/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_e4-f1_f6-g2_h2-i1_i4-j1_j6-k2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][a-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 1 types, 8 molecules

#9: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

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Details

Sequence detailsTHE SEQUENCE FOR CHAINS C,F,I,L BELONGS TO ISOFORM 2 OF FIBRINOGEN GAMMA CHAIN (UNP ENTRY P02679-2).

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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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2% PEG 3350, 0.2 M TMAO, 75 mM NaCl, 50 mM Tris, 1 mM CaCl2, 1 mM HPRPam, 1 mM GHRPam, 1 mM sodium azide, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2008 / Details: superbend
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 116461 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.102

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0061refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementResolution: 2.9→19.95 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.883 / Occupancy max: 1 / Occupancy min: 1 / SU B: 36.137 / SU ML: 0.338 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.489 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30917 5820 5 %RANDOM
Rwork0.25221 ---
obs0.25505 116461 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.575 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å20.6 Å2
2--2.38 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31283 0 550 0 31833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02232743
X-RAY DIFFRACTIONr_bond_other_d00.0222470
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.95944076
X-RAY DIFFRACTIONr_angle_other_deg1.9483.00454494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.32953872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84624.9091652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.466155702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.14115190
X-RAY DIFFRACTIONr_chiral_restr0.0710.24664
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0235993
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026437
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.904222321
X-RAY DIFFRACTIONr_mcbond_other1.08827924
X-RAY DIFFRACTIONr_mcangle_it5.184331037
X-RAY DIFFRACTIONr_scbond_it3.564213687
X-RAY DIFFRACTIONr_scangle_it5.246313012
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1501medium positional0.320.5
1501medium positional0.340
1501medium positional0.280
1501medium positional0.330
2044loose positional0.545
2044loose positional0.550
2044loose positional0.480
2044loose positional0.610
1501medium thermal7.232
1501medium thermal4.360
1501medium thermal2.60
1501medium thermal3.80
2044loose thermal6.4410
2044loose thermal3.680
2044loose thermal2.490
2044loose thermal3.220
LS refinement shellResolution: 2.901→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 19 -
Rwork0.264 400 -
obs--100 %
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)
16.71820.1889-1.63730.02310.02490.6820.09241.0895-0.04080.02320.02850.0321-0.0945-0.1127-0.12090.3693-0.0013-0.00180.3628-0.00470.3647-7.593316.9807-42.7224
25.78652.0684-2.57331.1551-0.49031.588-0.17540.088-0.8523-0.01120.1297-0.1644-0.06480.31180.04570.33590.0175-0.03690.377-0.06640.2722-80.97588.9859-18.0775
31.0467-0.0583-0.29740.02750.04660.13850.12060.31920.2278-0.06210.0043-0.057-0.07730.0495-0.12490.2871-0.0007-0.00190.28-0.00350.2822-44.995111.4572-27.6554
42.1582-0.08050.3110.8196-0.01691.96870.0969-0.0143-0.0798-0.0733-0.00510.0004-0.03080.1606-0.09180.05930.0204-0.01160.0355-0.01690.1597-95.11494.78927.4249
53.82030.1058-1.19070.0119-0.00610.4808-0.03590.51210.0137-0.03260.0499-0.03160.01410.0178-0.0140.27990.0014-0.00140.25670.00190.2736-41.867316.8978-32.0731
61.70640.4767-0.00531.8386-0.03891.51040.0166-0.1049-0.07750.0158-0.04020.10010.1172-0.08070.02360.09870.008-0.0201-0.08310.00750.0494-140.8027-8.072510.0963
77.4451-0.0367-2.03750.0540.14860.91460.3899-1.34220.74280.0209-0.1035-0.0177-0.12780.3249-0.28640.37270.0011-0.00130.36940.00240.3698120.19312.6991-69.1885
86.45470.5357-1.56050.98060.12610.53840.0983-0.6461-0.13850.0082-0.13190.10730.091-0.05740.03360.3889-0.0355-0.01120.4758-0.07440.1887195.20270.0681-91.2298
92.9986-0.4176-1.20430.08380.22870.6283-0.0086-0.38880.40950.04740.1005-0.01250.02570.081-0.09180.2923000.292300.2923158.96485.533-83.0682
102.54670.8105-0.18520.8370.05112.0264-0.0094-0.30760.12710.17880.0215-0.0207-0.05-0.0066-0.01210.22370.0492-0.0120.3697-0.06220.1478210.1003-7.6081-115.5453
111.8461-0.6323-0.37430.2410.19720.2706-0.1265-0.70340.14820.06140.1835-0.02130.0090.1736-0.0570.2433-0.0003-0.00030.24230.00010.2426200.05422.5512-97.3855
123.5754-1.0478-0.10331.75231.13193.00190.1407-0.8015-0.04390.1379-0.0531-0.33930.48140.1616-0.08760.10110.0166-0.01990.47550.02350.1276261.6536-21.3203-114.8281
136.0288-0.2008-1.56980.00860.07270.62280.29090.71240.32760.0361-0.0709-0.0489-0.0777-0.0719-0.220.3749-0.0026-0.00320.3673-0.00710.367327.4922-30.5304-82.3447
147.9470.0247-2.09060.7421-0.2620.69940.06920.5117-0.24080.0019-0.1445-0.08780.17760.02520.07530.30140.0470.01830.4720.08610.151-46.4784-33.9538-60.1915
151.8690.2268-0.57530.0279-0.06710.3298-0.01690.5202-0.0312-0.06240.0456-0.071-0.0281-0.0635-0.02880.2803-0.0011-0.00220.2752-0.00350.2749-10.2846-33.9297-68.6299
162.3071-0.34330.15371.1901-0.33431.59740.07140.2679-0.0638-0.10240.0156-0.0145-0.04190.0049-0.0870.0787-0.0358-0.00280.2250.02690.1266-61.2503-39.7074-35.1182
171.89540.0804-0.61550.0659-0.04520.30920.14640.38650.3538-0.04860.012-0.0411-0.0503-0.0126-0.15830.25620.0001-0.00310.2355-0.00350.2451-51.6922-34.1001-53.7264
183.33220.75630.24432.5505-0.86721.85330.04340.5556-0.2507-0.41830.03620.34370.3324-0.0472-0.07960.17670.0072-0.05050.2463-0.07790.1967-112.5471-53.4674-35.4082
197.976-0.5281-1.89920.05770.2330.9590.3203-1.28530.4235-0.1557-0.07360.0198-0.09830.2024-0.24670.38570.0009-0.00180.37490.00420.3804155.9658-44.6791-105.8683
205.2632-0.14-2.1670.71720.02910.95360.1512-0.28980.08650.095-0.05880.1005-0.0458-0.1778-0.09240.3415-0.0296-0.00240.4541-0.02520.1695229.8177-55.1282-132.0335
212.5471-0.3568-0.79640.08580.17230.3522-0.0242-0.59960.17830.04430.04960.04650.00790.1085-0.02540.27330-0.00070.26830.0020.2712194.4076-50.7755-122.3018
223.35240.11940.48740.9051-0.23331.96510.0089-0.17180.02630.11840.061-0.0251-0.0091-0.1832-0.06990.17730.01770.02460.2744-0.00160.1064243.8539-58.4279-157.6609
234.9232-0.234-2.02160.02330.14531.02950.1538-1.01160.43660.01360.0235-0.0006-0.0440.2291-0.17730.3698-0.0009-0.00110.3619-0.00190.3659191.4011-45.8424-117.4431
242.0689-0.43250.26192.19310.06812.01720.06380.1007-0.1198-0.0098-0.0482-0.19490.23210.0386-0.01550.1067-0.00110.0065-0.0116-0.00220.1071289.7523-71.3264-160.6678
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 150
2X-RAY DIFFRACTION2A151 - 200
3X-RAY DIFFRACTION3B58 - 248
4X-RAY DIFFRACTION4B249 - 458
5X-RAY DIFFRACTION5C14 - 162
6X-RAY DIFFRACTION6C163 - 394
7X-RAY DIFFRACTION7D27 - 149
8X-RAY DIFFRACTION8D150 - 200
9X-RAY DIFFRACTION9E58 - 248
10X-RAY DIFFRACTION10E249 - 458
11X-RAY DIFFRACTION11F14 - 287
12X-RAY DIFFRACTION12F288 - 395
13X-RAY DIFFRACTION13G27 - 150
14X-RAY DIFFRACTION14G151 - 200
15X-RAY DIFFRACTION15H58 - 248
16X-RAY DIFFRACTION16H249 - 458
17X-RAY DIFFRACTION17I2 - 288
18X-RAY DIFFRACTION18I289 - 395
19X-RAY DIFFRACTION19J27 - 150
20X-RAY DIFFRACTION20J151 - 200
21X-RAY DIFFRACTION21K58 - 249
22X-RAY DIFFRACTION22K250 - 458
23X-RAY DIFFRACTION23L5 - 163
24X-RAY DIFFRACTION24L164 - 395

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