[English] 日本語
Yorodumi
- PDB-4wza: Asymmetric Nucleotide Binding in the Nitrogenase Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4wza
TitleAsymmetric Nucleotide Binding in the Nitrogenase Complex
Components
  • (Nitrogenase molybdenum-iron protein ...) x 2
  • Nitrogenase iron protein 1
KeywordsOXIDOREDUCTASE / Nitrogenase / Nucleotide binding / Asymetry / Complex
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / carbonyl sulfide nitrogenase activity / nitrogenase activity / nitrogen fixation / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / Nitrogenase molybdenum-iron protein beta chain, N-terminal ...Nitrogenase Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / Nitrogenase iron protein NifH / NifH/frxC family / NifH/chlL conserved site / 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family / NifH/frxC family signature 2. / NifH/frxC family signature 1. / NIFH_FRXC family profile. / Nitrogenase molybdenum-iron protein beta chain, N-terminal / Domain of unknown function (DUF3364) / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain / Nitrogenase component 1, alpha chain / Nitrogenase component 1, conserved site / Nitrogenases component 1 alpha and beta subunits signature 2. / Nitrogenases component 1 alpha and beta subunits signature 1. / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase / Nitrogenase molybdenum iron protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-DIPHOSPHATE / FE(8)-S(7) CLUSTER / : / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / IRON/SULFUR CLUSTER / Nitrogenase iron protein 1 / Nitrogenase molybdenum-iron protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8995 Å
AuthorsTezcan, F.A. / Kaiser, J.T. / Howard, J.B. / Rees, D.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM099813 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM045162 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Structural evidence for asymmetrical nucleotide interactions in nitrogenase.
Authors: Tezcan, F.A. / Kaiser, J.T. / Howard, J.B. / Rees, D.C.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_nat / pdbx_audit_support ...entity_src_nat / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _refine_hist.d_res_high / _struct_conn.pdbx_dist_value / _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.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrogenase molybdenum-iron protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
C: Nitrogenase molybdenum-iron protein alpha chain
D: Nitrogenase molybdenum-iron protein beta chain
E: Nitrogenase iron protein 1
F: Nitrogenase iron protein 1
G: Nitrogenase iron protein 1
H: Nitrogenase iron protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)353,03026
Polymers346,9238
Non-polymers6,10718
Water39,5972198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51770 Å2
ΔGint-419 kcal/mol
Surface area90310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.201, 120.412, 264.318
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Nitrogenase molybdenum-iron protein ... , 2 types, 4 molecules ACBD

#1: Protein Nitrogenase molybdenum-iron protein alpha chain / Dinitrogenase / Nitrogenase component I


Mass: 53999.574 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07328, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase / Nitrogenase component I


Mass: 59404.684 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P07329, nitrogenase

-
Protein , 1 types, 4 molecules EFGH

#3: Protein
Nitrogenase iron protein 1 / Nitrogenase Fe protein 1 / Nitrogenase component II / Nitrogenase reductase


Mass: 30028.598 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase

-
Non-polymers , 9 types, 2216 molecules

#4: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


Mass: 206.150 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O7
#5: Chemical ChemComp-ICS / iron-sulfur-molybdenum cluster with interstitial carbon


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9
#6: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#7: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#9: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#11: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2198 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18-22% PEG 8000, 0-50 mM NaCl, 100 mM Tris pH 8.5, 10 mM sodium dithionite, 10 mM MgCl2, 5 mM AMPPCP, 5 mM ADP

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8995→19.85 Å / Num. obs: 269523 / % possible obs: 98 % / Redundancy: 3.6 % / Biso Wilson estimate: 19.8 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.048 / Net I/σ(I): 13.5 / Num. measured all: 972879
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.8995-1.932.70.591.931434115900.6410.486.6
10.41-19.853.20.02640504815820.9990.01685.1

-
Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.2.14data scaling
PDB_EXTRACT3.15data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M1N, 1M34

1m1n

1m34


Resolution: 1.8995→19.841 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 13599 5.05 %Random selection
Rwork0.145 255794 --
obs0.1471 269393 97.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.31 Å2 / Biso mean: 28.5776 Å2 / Biso min: 8.3 Å2
Refinement stepCycle: final / Resolution: 1.8995→19.841 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24215 0 246 2184 26645
Biso mean--24.18 34.9 -
Num. residues----3086
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0125037
X-RAY DIFFRACTIONf_angle_d1.50134221
X-RAY DIFFRACTIONf_chiral_restr0.0513655
X-RAY DIFFRACTIONf_plane_restr0.0064350
X-RAY DIFFRACTIONf_dihedral_angle_d14.5519440
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8995-1.92110.30323720.25326916728880
1.9211-1.94360.27213840.23357804818890
1.9436-1.96730.2784680.22798032850093
1.9673-1.99220.26444530.21088136858995
1.9922-2.01840.24964290.20418249867895
2.0184-2.0460.23614480.19578354880296
2.046-2.07520.2384480.18438420886897
2.0752-2.10610.23434940.17188503899799
2.1061-2.1390.21164400.16588552899299
2.139-2.1740.21394490.16558604905399
2.174-2.21150.21644490.15868552900199
2.2115-2.25160.2044560.15538614907099
2.2516-2.29490.20485030.14778563906699
2.2949-2.34170.1944410.14578620906199
2.3417-2.39250.19034390.14438621906099
2.3925-2.44810.19344550.13988655911099
2.4481-2.50920.19854300.13858660909099
2.5092-2.57690.18874610.13986149075100
2.5769-2.65250.18024470.13786709117100
2.6525-2.73790.19694560.141186929148100
2.7379-2.83550.19324680.146986769144100
2.8355-2.94870.18834630.143786929155100
2.9487-3.08240.19034940.146987169210100
3.0824-3.24430.17674470.141487359182100
3.2443-3.44660.19074530.140387599212100
3.4466-3.71110.16494210.130788069227100
3.7111-4.08160.14764840.114487859269100
4.0816-4.66550.14384870.109587969283100
4.6655-5.85290.14824540.123789119365100
5.8529-19.84230.15295060.13599087959399
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)
12.3901-0.85630.14371.84040.30692.6657-0.0667-0.1879-0.61170.09080.0531-0.20450.59970.10210.03250.34720.00180.01990.20610.14430.5387-10.2108-54.729938.6853
21.05870.1348-0.3030.4822-0.14320.8611-0.03530.0601-0.1017-0.03970.06280.07720.0496-0.091-0.04220.1511-0.0278-0.01130.09940.01860.1151-25.0546-25.904119.4394
32.05030.1471-0.19791.2867-0.09921.8036-0.06070.1718-0.1625-0.23810.1350.16210.1076-0.3732-0.06280.2209-0.0537-0.03110.19560.01080.1804-34.6428-31.978116.9334
41.64630.064-0.38840.60910.18680.8899-0.0960.3239-0.2739-0.30460.0494-0.02270.0824-0.02080.04340.33-0.05390.02210.1679-0.0520.2177-15.3386-38.45774.6425
51.631-0.46820.03580.41360.17670.8348-0.09760.2015-0.6208-0.20520.063-0.03480.3039-0.02590.02430.3685-0.02790.05640.1517-0.05360.3305-10.0054-47.77437.997
61.43330.1108-0.14940.5777-0.12930.7753-0.08030.1456-0.4039-0.1510.0697-0.20310.24670.07020.00770.27640.03950.05690.1533-0.02770.33832.3185-44.544918.6142
72.6233-0.0594-0.34022.01790.33111.7809-0.0834-0.2645-0.46320.05650.0405-0.1950.11430.08770.04980.2580.01610.010.20620.12560.375-4.7403-47.337336.7131
81.35890.3537-0.13521.00210.2671.42990.0191-0.1597-0.32330.01850.0039-0.07290.01470.0127-0.02930.16880.03450.00810.13220.02930.2176-1.3215-33.620230.6071
91.3781.09462.13142.6244.50119.64980.1633-0.0414-0.2670.16670.056-0.2840.41330.1795-0.23490.17120.03670.01120.16630.04640.27549.0861-31.303531.0509
103.33740.88982.38751.56490.4593.6498-0.14630.4553-0.1413-0.34010.1461-0.23410.01540.2940.00090.2979-0.02730.09890.2282-0.0310.18911.3784-26.91035.4507
111.5174-0.0472-0.59111.27010.30922.5661-0.02640.2120.1076-0.29370.05550.1468-0.0801-0.0657-0.02680.164-0.0379-0.05150.12130.02740.1235-24.0155-11.81559.702
120.96440.2107-0.00030.4921-0.12420.54470.018-0.1445-0.16780.02730.00380.03710.1441-0.0076-0.02810.17880.007200.16620.07250.1718-22.6228-31.897941.5729
130.86080.21750.22722.13620.0870.35360.0459-0.4342-0.03180.2455-0.06240.07530.1354-0.10380.01640.1755-0.020.02920.27880.09730.1796-29.7491-26.700951.2188
140.90150.306-0.45660.9055-0.28960.760.0578-0.2972-0.00880.24-0.0725-0.0258-0.03140.11240.02320.1831-0.00410.00190.28270.02970.1154-14.7145-9.160753.4462
150.53610.0029-0.67840.15480.25531.2314-0.008-0.1641-0.1010.0869-0.0177-0.1070.00580.17530.02580.19490.0073-0.01240.27260.07830.1664-8.8089-21.488750.7707
161.60.9544-0.76541.8088-0.70912.50920.0864-0.19740.03450.249-0.06020.2037-0.0544-0.273-0.04060.16540.02280.03010.26250.01250.1326-25.9864-9.558653.4805
170.61590.4678-0.03440.72190.07490.34680.0027-0.12940.08370.0286-0.00960.0901-0.0049-0.05420.00980.12810.03790.01060.18470.00260.1506-13.98153.485239.7653
180.9039-0.1286-0.0020.90270.39790.9249-0.03750.06550.0368-0.07140.02140.0838-0.0386-0.00880.01220.11310.0051-0.00380.12290.03370.128-16.5839-4.810324.7969
191.9860.7267-1.88670.6549-0.60822.5759-0.0730.07750.0424-0.08350.07760.04890.1499-0.04030.00110.12580.0233-0.00920.14460.01830.13830.75873.619424.4693
202.4555-1.12410.12082.83-1.22833.4726-0.0905-0.26280.38340.17030.1290.2381-0.5023-0.223-0.00570.28540.0456-0.02250.2102-0.12150.354710.678542.224442.2407
210.9227-0.04080.13170.37850.04510.5116-0.03140.14560.1376-0.08810.0106-0.0179-0.07630.03650.02350.133-0.00430.00410.11270.03210.110923.487421.004515.4844
221.0604-0.0109-0.22140.3601-0.12660.706-0.04430.19890.2734-0.06960.04670.0741-0.1552-0.1078-0.00480.21150.0205-0.03670.1410.06220.2232.493635.157110.9545
231.09390.47920.26570.70010.05030.6382-0.0172-0.10740.25770.03760.00750.0978-0.1277-0.08260.0060.16790.04890.00690.1519-0.01560.20473.460630.48532.7022
241.791.92-2.40324.4602-4.74265.08260.1741-0.14610.1880.27630.01140.263-0.38170.0391-0.22520.13260.0431-0.00920.1558-0.01040.203-8.563519.436632.7914
251.1617-0.4188-0.06020.9384-0.03181.04150.02090.2654-0.0427-0.1802-0.05550.0527-0.0151-0.05060.0350.145-0.03120.0060.13050.00680.116613.97327.91828.858
261.32580.35850.10870.45960.0320.3930.0023-0.19030.1240.0441-0.03310.027-0.0914-0.05270.02980.14240.02680.00110.1726-0.0110.129423.027119.188243.5909
270.45940.3649-0.18120.85140.1240.48810.1025-0.314-0.03580.181-0.1234-0.10270.03230.01030.01690.16080.0008-0.02830.26830.03410.130624.45336.732953.2078
280.80670.42920.2210.4704-0.50751.61770.0533-0.36250.06710.1334-0.09030.06950.0657-0.1650.02830.15-0.00830.01240.2883-0.01090.13229.10128.191951.9069
290.880.69030.50740.95110.40640.40970.1215-0.2057-0.17690.1526-0.108-0.15730.0463-0.0049-0.02380.16260.0211-0.02180.24160.07770.166418.4619-11.345850.4009
300.68820.1837-0.15760.7627-0.09620.7547-0.0489-0.0425-0.1208-0.00820.0247-0.11780.08160.04920.02170.11320.02220.01920.11120.01870.142417.6587-8.221526.5403
311.80360.46341.58560.63290.26212.4725-0.0569-0.0353-0.0793-0.0901-0.0036-0.0828-0.1004-0.14220.08790.11740.02180.02180.10350.02450.1106-0.2636-14.930223.8169
321.42210.6821-0.17431.4635-0.32320.40080.1843-0.2519-0.8453-0.23620.08440.2050.1526-0.0419-0.2120.3945-0.0621-0.12130.27220.14480.5596-50.3737-51.944525.9026
331.52371.76820.58433.60971.5320.88420.03290.073-0.5098-0.15510.18260.05970.3026-0.0113-0.13210.3139-0.0282-0.07910.15440.09040.452-44.1929-48.723826.927
344.53890.53521.19561.2831-1.2211.83960.20460.1252-0.5888-0.19530.06230.14730.21720.1495-0.17880.3097-0.0215-0.06610.16630.03250.3368-51.913-43.477719.6352
351.447-1.2317-0.45061.13870.05772.51990.2861-0.2825-0.63680.1833-0.1030.2483-0.4093-0.2703-0.18590.4699-0.0112-0.04530.37550.17630.5268-66.5307-42.797724.6533
362.5643-1.1729-1.44410.81020.43592.08880.37130.2765-0.2765-0.3658-0.07110.2467-0.2201-0.3576-0.28520.40120.0296-0.12130.35660.05140.4586-70.5241-37.679421.2857
372.4437-0.5028-1.15681.8541-0.11882.25180.13470.07220.28610.10620.09220.2249-0.3731-0.1783-0.21090.23440.02480.03550.25540.1140.2949-54.7539-20.499941.5921
383.222-0.3932-0.86420.8566-1.11953.25370.0173-0.3482-0.46280.13120.05330.20020.10480.0316-0.06590.2039-0.0060.00320.27890.09640.3003-51.7756-32.483747.6472
391.86260.81490.86410.7872-0.50952.38170.2822-0.3816-0.51740.05720.25480.37130.3698-0.4848-0.44270.3248-0.0102-0.02730.43880.24180.5547-65.391-37.465850.8415
402.330.52830.18583.0037-0.73021.10970.1359-0.03980.59530.04220.0066-0.1928-0.16990.0452-0.1180.2744-0.02640.01980.13890.02430.343756.120839.798928.2207
411.68021.7968-0.82562.2394-0.54581.33710.18410.00780.60020.1655-0.22720.0095-0.3396-0.02860.02910.26670.01390.00810.16620.01440.411841.945240.27732.7144
423.64231.5167-1.59182.49810.5231.82830.11550.37620.5217-0.2295-0.11980.2191-0.297-0.10830.02810.2103-0.0002-0.02740.15730.04110.235546.275134.711724.0668
436.03250.3354-0.24662.38010.08061.6989-0.0940.53090.5466-0.16570.03310.0147-0.03190.07040.04960.2058-0.019-0.00220.14140.05010.166654.804827.94422.4953
441.8827-0.0937-0.03852.03220.73281.6704-0.0619-0.00810.46410.03230.0835-0.2938-0.1030.2548-0.02640.1802-0.01080.00720.20480.03140.320667.037131.600525.4462
458.28970.58545.24433.2256-0.80467.61840.05450.27760.1007-0.2053-0.13510.00250.06640.15580.04970.17920.06480.04970.19260.01760.250976.603813.988830.6128
462.5443-0.71661.3851.4542-0.11382.8550.14010.0103-0.21110.03340.0066-0.02360.33870.1475-0.13610.17070.0247-0.0040.1604-0.00480.188755.08487.560343.0198
472.5796-0.29690.02430.80350.38442.31150.0125-0.34860.45440.06970.123-0.2043-0.20010.125-0.10740.20740.0002-0.00290.2168-0.06340.266760.577221.970852.133
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 49 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 153 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 154 through 190 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 275 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 317 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 318 through 391 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 392 through 416 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 417 through 451 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 452 through 480 )A0
10X-RAY DIFFRACTION10chain 'B' and (resid 2 through 31 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 32 through 70 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 71 through 161 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 162 through 215 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 216 through 247 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 248 through 277 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 278 through 320 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 321 through 399 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 400 through 485 )B0
19X-RAY DIFFRACTION19chain 'B' and (resid 486 through 523 )B0
20X-RAY DIFFRACTION20chain 'C' and (resid 4 through 49 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 50 through 275 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 276 through 346 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 347 through 451 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 452 through 480 )C0
25X-RAY DIFFRACTION25chain 'D' and (resid 2 through 70 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 71 through 161 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 162 through 247 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 248 through 277 )D0
29X-RAY DIFFRACTION29chain 'D' and (resid 278 through 362 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 363 through 485 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 486 through 523 )D0
32X-RAY DIFFRACTION32chain 'E' and (resid 1 through 74 )E0
33X-RAY DIFFRACTION33chain 'E' and (resid 75 through 111 )E0
34X-RAY DIFFRACTION34chain 'E' and (resid 112 through 154 )E0
35X-RAY DIFFRACTION35chain 'E' and (resid 155 through 234 )E0
36X-RAY DIFFRACTION36chain 'E' and (resid 235 through 276 )E0
37X-RAY DIFFRACTION37chain 'F' and (resid 1 through 111 )F0
38X-RAY DIFFRACTION38chain 'F' and (resid 112 through 172 )F0
39X-RAY DIFFRACTION39chain 'F' and (resid 173 through 271 )F0
40X-RAY DIFFRACTION40chain 'G' and (resid 1 through 56 )G0
41X-RAY DIFFRACTION41chain 'G' and (resid 57 through 97 )G0
42X-RAY DIFFRACTION42chain 'G' and (resid 98 through 132 )G0
43X-RAY DIFFRACTION43chain 'G' and (resid 133 through 154 )G0
44X-RAY DIFFRACTION44chain 'G' and (resid 155 through 260 )G0
45X-RAY DIFFRACTION45chain 'G' and (resid 261 through 276 )G0
46X-RAY DIFFRACTION46chain 'H' and (resid 1 through 111 )H0
47X-RAY DIFFRACTION47chain 'H' and (resid 112 through 271 )H0

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more