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- PDB-4wzb: Crystal Structure of MgAMPPCP-bound Av2-Av1 complex -

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Basic information

Entry
Database: PDB / ID: 4wzb
TitleCrystal Structure of MgAMPPCP-bound Av2-Av1 complex
Components
  • (Nitrogenase molybdenum-iron protein ...) x 2
  • Nitrogenase iron protein 1
KeywordsOXIDOREDUCTASE / NITROGEN FIXATION / IRON-SULFUR / METAL-BINDING / MOLYBDENUM
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / : / 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 / 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 / Resolution: 2.3 Å
AuthorsTezcan, F.A. / Kaiser, J.T. / Mustafi, D. / Walton, M.Y. / 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
Citation
Journal: Science / Year: 2005
Title: Nitrogenase complexes: multiple docking sites for a nucleotide switch protein.
Authors: Tezcan, F.A. / Kaiser, J.T. / Mustafi, D. / Walton, M.Y. / Howard, J.B. / Rees, D.C.
#1: Journal: Science / Year: 2005
Title: Nitrogenase complexes: multiple docking sites for a nucleotide switch protein.
Authors: Tezcan, F.A. / Kaiser, J.T. / Mustafi, D. / Walton, M.Y. / Howard, J.B. / Rees, D.C.
History
DepositionNov 19, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 25, 2015ID: 2AFK
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Feb 28, 2024Group: 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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ncs_dom_lim
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 / _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 / _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: 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)351,29526
Polymers345,0338
Non-polymers6,26318
Water16,934940
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area51250 Å2
ΔGint-402 kcal/mol
Surface area90890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.533, 120.894, 264.834
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12chain B
22chain D
13chain E
23chain F
33chain G
43chain H

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETGLUGLUchain AAA4 - 4801 - 477
21SERSERGLUGLUchain CCC5 - 4802 - 477
12SERSERARGARGchain BBB2 - 5231 - 522
22SERSERARGARGchain DDD2 - 5231 - 522
13ALAALAGLUGLUchain EEE1 - 2701 - 270
23ALAALAGLUGLUchain FFF1 - 2631 - 263
33ALAALAGLYGLYchain GGG1 - 2721 - 272
43ALAALAASPASPchain HHH1 - 2621 - 262

NCS ensembles :
ID
1
2
3

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Components

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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

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Protein , 1 types, 4 molecules EFGH

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


Mass: 29556.002 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / References: UniProt: P00459, nitrogenase

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Non-polymers , 8 types, 958 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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#8: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#9: Chemical
ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#10: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 940 / 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: 2.56 Å3/Da / Density % sol: 52.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 8000, TRIS, SODIUM CHLORIDE, MAGNESIUM CHLORIDE, DITHIONITE, AMPPCP, PH 8.5

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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: Nov 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 140701 / % possible obs: 89.2 % / Redundancy: 3.4 % / Rsym value: 0.123 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.5 Å / % possible all: 85.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.3→49.382 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 9906 7.04 %
Rwork0.2036 130772 -
obs0.2073 140678 89.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.14 Å2 / Biso mean: 32.8112 Å2 / Biso min: 12.42 Å2
Refinement stepCycle: final / Resolution: 2.3→49.382 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23976 0 240 940 25156
Biso mean--32.25 29.76 -
Num. residues----3056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01224779
X-RAY DIFFRACTIONf_angle_d1.60633877
X-RAY DIFFRACTIONf_chiral_restr0.0583617
X-RAY DIFFRACTIONf_plane_restr0.0074304
X-RAY DIFFRACTIONf_dihedral_angle_d15.2499342
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4662X-RAY DIFFRACTION9.139TORSIONAL
12C4662X-RAY DIFFRACTION9.139TORSIONAL
21B5133X-RAY DIFFRACTION9.139TORSIONAL
22D5133X-RAY DIFFRACTION9.139TORSIONAL
31E4998X-RAY DIFFRACTION9.139TORSIONAL
32F4998X-RAY DIFFRACTION9.139TORSIONAL
33G4998X-RAY DIFFRACTION9.139TORSIONAL
34H4998X-RAY DIFFRACTION9.139TORSIONAL
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 (%)
2.3-2.32610.31393220.22914130445286
2.3261-2.35350.28393240.21884117444185
2.3535-2.38220.28213100.22324156446686
2.3822-2.41240.29053030.22134115441884
2.4124-2.44410.27763010.2244129443086
2.4441-2.47760.28783110.21464074438584
2.4776-2.5130.29342990.22274092439184
2.513-2.55050.29133170.21064090440785
2.5505-2.59030.29282930.2054050434383
2.5903-2.63280.26743180.19954039435783
2.6328-2.67820.26293190.20524028434784
2.6782-2.72690.29533190.21853978429782
2.7269-2.77930.28232890.21714020430982
2.7793-2.83610.29523200.21043952427282
2.8361-2.89770.27012830.20674011429482
2.8977-2.96510.26713220.20263946426881
2.9651-3.03930.2562890.22173959424881
3.0393-3.12140.28933010.23264017431882
3.1214-3.21330.29483230.21664141446485
3.2133-3.3170.26913270.22084438476591
3.317-3.43550.27983620.23824669503196
3.4355-3.5730.27414050.22074839524499
3.573-3.73560.253780.207348525230100
3.7356-3.93240.23733810.207149065287100
3.9324-4.17870.25213400.206848965236100
4.1787-4.50110.23173710.194149555326100
4.5011-4.95370.22843460.179749715317100
4.9537-5.66960.22633820.179749675349100
5.6696-7.13970.23833610.179450555416100
7.1397-49.39320.17383900.15615180557099

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