[English] 日本語
Yorodumi
- PDB-8p8g: Nitrogenase MoFe protein from A. vinelandii beta double mutant D3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p8g
TitleNitrogenase MoFe protein from A. vinelandii beta double mutant D353G/D357G
Components
  • Nitrogenase molybdenum-iron protein beta chain
  • Nitrogenase protein alpha chain
KeywordsOXIDOREDUCTASE / Molybdenum nitrogenase / N2-fixation / FeMocofactor / metal binding site / P cluster / NH3 production
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / iron-sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER, OXIDIZED / FE(8)-S(7) CLUSTER / 1,4-DIETHYLENE DIOXIDE / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / Nitrogenase protein alpha chain / Nitrogenase molybdenum-iron protein beta chain
Similarity search - Component
Biological speciesAzotobacter vinelandii DJ (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMaslac, N. / Wagner, T.
Funding support Germany, Switzerland, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)WA 4053/1-1 Germany
Swiss National Science Foundation180544 Switzerland
CitationJournal: Jacs Au / Year: 2023
Title: The Mononuclear Metal-Binding Site of Mo-Nitrogenase Is Not Required for Activity.
Authors: Cadoux, C. / Maslac, N. / Di Luzio, L. / Ratcliff, D. / Gu, W. / Wagner, T. / Milton, R.D.
History
DepositionJun 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nitrogenase protein alpha chain
B: Nitrogenase molybdenum-iron protein beta chain
C: Nitrogenase protein alpha chain
D: Nitrogenase molybdenum-iron protein beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,98153
Polymers231,7744
Non-polymers7,20749
Water39,1472173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39720 Å2
ΔGint-140 kcal/mol
Surface area57810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.486, 74.469, 208.467
Angle α, β, γ (deg.)90.00, 103.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1476-

HOH

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein Nitrogenase protein alpha chain


Mass: 56467.234 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / Tissue: / / Cell line: / / Gene: nifD / Organ: /
Plasmid details: Produces the MoFe protein with a poly(histidine)8 tag on the N-term of NifD and a double substituted NifK mutant
Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DGZ7
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase


Mass: 59419.809 Da / Num. of mol.: 2 / Mutation: D353G and D357G
Source method: isolated from a genetically manipulated source
Details: The double substitution D353G and D357G was introduced.
Source: (gene. exp.) Azotobacter vinelandii DJ (bacteria) / Strain: DJ / Tissue: / / Cell line: / / Gene: nifK, Avin_01400 / Organ: /
Plasmid details: Produces the MoFe protein with a poly(histidine)8 tag on the N-term of NifD and a double substituted NifK mutant
Production host: Azotobacter vinelandii DJ (bacteria) / References: UniProt: C1DGZ8, nitrogenase

-
Non-polymers , 10 types, 2222 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-HCA / 3-HYDROXY-3-CARBOXY-ADIPIC ACID


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


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-1CL / FE(8)-S(7) CLUSTER, OXIDIZED


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical ChemComp-CLF / FE(8)-S(7) CLUSTER


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2173 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.06 %
Description: Brown plate, which appeared in a couple of weeks
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: The beta-D353G/D357G MoFe-protein was crystallized anaerobically at 17.5 mg/mL under 100% N2 atmosphere. The protein was spotted as a sitting drop to 96-Well MRC 2-Drop polystyrene ...Details: The beta-D353G/D357G MoFe-protein was crystallized anaerobically at 17.5 mg/mL under 100% N2 atmosphere. The protein was spotted as a sitting drop to 96-Well MRC 2-Drop polystyrene Crystallization Plates (SWISSCI) containing 90 uL of crystallization solution in the reservoir. Each drop contained 0.5 uL of protein sample and 0.5 uL of crystallization solution. Crystals were obtained in the crystallization solution containing 10 % w/v Polyethylene glycol 10,000; 2 % v/v 1,4-Dioxane; 100 mM tri-Sodium citrate; pH 5.6, and 1 mM polyoxotungstate [TeW6O24]6- (TEW). Sealed plates were stored inside a Coy anaerobic chamber filled with an atmosphere of N2:H2 97:3 at 20 C. Crystals were soaked in the crystallization solution supplemented with 30% v/v ethylene glycol for a few seconds before freezing in liquid nitrogen.
PH range: / / Temp details: /

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.55→101.46 Å / Num. obs: 176043 / % possible obs: 94 % / Redundancy: 8.1 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.066 / Rrim(I) all: 0.189 / Net I/σ(I): 8.1
Reflection shellResolution: 1.55→1.76 Å / Redundancy: 9.3 % / Rmerge(I) obs: 1.89 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 8391 / CC1/2: 0.566 / Rpim(I) all: 0.652 / Rrim(I) all: 2.001 / % possible all: 80.5

-
Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→48.32 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.28 / Stereochemistry target values: ML
Details: The model was manually rebuilt with COOT and further refined with PHENIX. During the refinement, a translational-libration screw was applied with the model containing hydrogens added in the ...Details: The model was manually rebuilt with COOT and further refined with PHENIX. During the refinement, a translational-libration screw was applied with the model containing hydrogens added in the riding position during the last refinement cycles. Hydrogens were removed in the final deposited model.
RfactorNum. reflection% reflection
Rfree0.1872 8763 4.98 %
Rwork0.155 --
obs0.1566 175938 48.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.62 Å2
Refinement stepCycle: LAST / Resolution: 1.55→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15912 0 285 2176 18373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01216703
X-RAY DIFFRACTIONf_angle_d1.03522651
X-RAY DIFFRACTIONf_dihedral_angle_d15.6296193
X-RAY DIFFRACTIONf_chiral_restr0.0612347
X-RAY DIFFRACTIONf_plane_restr0.012877
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.508870.2917172X-RAY DIFFRACTION2
1.57-1.590.469240.27334X-RAY DIFFRACTION3
1.59-1.610.3035230.2612466X-RAY DIFFRACTION4
1.61-1.630.3693470.2659607X-RAY DIFFRACTION5
1.63-1.650.227360.2613734X-RAY DIFFRACTION6
1.65-1.670.219370.2532895X-RAY DIFFRACTION8
1.67-1.690.2364660.2491070X-RAY DIFFRACTION9
1.69-1.720.2807690.24491345X-RAY DIFFRACTION12
1.72-1.750.2471750.23751526X-RAY DIFFRACTION13
1.75-1.770.2677970.241785X-RAY DIFFRACTION16
1.77-1.80.24541210.24161969X-RAY DIFFRACTION17
1.8-1.840.24321260.22772264X-RAY DIFFRACTION20
1.84-1.870.25781100.21562685X-RAY DIFFRACTION23
1.87-1.910.24211680.21373091X-RAY DIFFRACTION27
1.91-1.950.23292090.20613597X-RAY DIFFRACTION32
1.95-20.20432240.19164241X-RAY DIFFRACTION37
2-2.050.20272640.19434982X-RAY DIFFRACTION44
2.05-2.10.27783250.23066038X-RAY DIFFRACTION53
2.1-2.170.22964140.18847602X-RAY DIFFRACTION67
2.17-2.240.2254450.1928785X-RAY DIFFRACTION77
2.24-2.320.23955060.19869890X-RAY DIFFRACTION86
2.32-2.410.20956100.172510918X-RAY DIFFRACTION95
2.41-2.520.20675680.169711285X-RAY DIFFRACTION99
2.52-2.650.19486060.167411459X-RAY DIFFRACTION100
2.65-2.820.19325330.157411504X-RAY DIFFRACTION100
2.82-3.030.19116000.144511529X-RAY DIFFRACTION100
3.03-3.340.1786160.132911488X-RAY DIFFRACTION100
3.34-3.820.14875870.118911576X-RAY DIFFRACTION100
3.82-4.810.12686140.103111566X-RAY DIFFRACTION100
4.81-48.320.17186360.15211772X-RAY DIFFRACTION100
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)
11.0038-0.4195-0.1561.27910.21770.5937-0.0378-0.22830.11570.22410.0360.0933-0.0338-0.19290.00010.1586-0.02780.02310.27150.00820.094624.924.182391.4121
20.8082-0.1563-0.37360.7109-0.11820.3903-0.0013-0.1344-0.21290.06820.01770.06380.313-0.1830.01380.2158-0.0846-0.02530.15030.05620.1334.2895-20.432579.2988
30.73850.08150.02470.6684-0.04590.80850.0175-0.1313-0.09250.13360.0054-0.04440.1634-0.0126-0.01920.1308-0.019-0.02160.13830.0170.072947.7463-6.628491.6231
40.79490.1057-0.04680.7927-0.01110.899-0.0046-0.09990.13190.0630.00460.0579-0.2009-0.14810.0020.11490.02080.01210.1138-0.01920.082936.595315.090981.4913
51.1430.01040.07491.01290.25230.72620.002-0.0462-0.1309-0.04820.0753-0.14520.16920.0684-0.05870.1329-0.0007-0.02080.08060.03310.040448.418-12.662970.3308
60.39020.1294-0.17580.2054-0.11990.25550.0117-0.1959-0.02840.0983-0.00620.16650.0636-0.3379-0.05050.0341-0.15150.10320.44660.06410.147110.1246-6.034680.8261
70.82780.01020.00780.4996-0.11320.3340.0239-0.04650.04490.0658-0.02240.22820.0363-0.3163-0.02610.0808-0.0860.03150.45270.01560.23612.1566-4.707759.0284
80.33910.26740.22860.23140.17640.1550.0116-0.04180.07820.0318-0.00640.17360.024-0.25260.00860.1032-0.03590.01740.43890.02050.21924.74251.831263.9165
91.62760.1731-0.84590.1658-0.22050.5539-0.0009-0.062-0.16270.04420.00090.13380.1439-0.20290.0340.1656-0.19470.01220.37460.04540.23783.4212-16.30660.1976
100.28180.04470.02210.22440.01730.41320.0427-0.0246-0.0852-0.0123-0.00120.06730.193-0.2234-0.0320.1438-0.0935-0.00810.15520.02580.143524.8814-14.528452.064
112.23240.206-0.71750.4096-0.09990.7098-0.0118-0.0853-0.01230.02080.0213-0.02060.0728-0.0425-0.01350.0997-0.0379-0.00650.0528-0.00190.080138.0489-4.952242.461
121.9009-0.5448-0.09972.52990.87790.97080.06960.2839-0.2396-0.2888-0.04820.25470.2005-0.1955-0.00190.2056-0.045-0.05020.1474-0.00410.123124.1402-7.22751.1823
130.6668-0.05610.2040.6495-0.07950.4588-0.02340.09540.0968-0.03870.0306-0.081-0.16910.1408-0.00730.1213-0.04480.01130.0549-0.0040.090950.849511.216421.5721
140.62850.0246-0.00480.6486-0.03970.7210.01310.0656-0.0923-0.01070.0263-0.02610.16820.0715-0.02770.126-0.0209-0.01620.0375-0.01930.077646.504-12.189515.1577
150.5196-0.59520.03070.89040.15870.9544-0.0063-0.0479-0.18190.06880.0060.13920.1286-0.2240.00690.1674-0.0894-0.02220.04670.01520.133529.5601-14.532328.8723
160.8935-0.10730.02160.60930.19980.68110.0569-0.0597-0.01390.0911-0.0146-0.11260.0660.1655-0.02630.1009-0.0197-0.02320.0790.00570.065856.838-1.200235.5801
170.37830.0040.27020.6672-0.25891.0865-0.01230.04630.086-0.08960.00520.0315-0.1153-0.1170.00530.10570.01730.0040.05580.02450.093427.876913.357316.5644
180.16070.01810.0230.13550.19470.90210.00470.06340.1246-0.03190.00570.0985-0.263-0.2184-0.00540.18610.07420.0030.09120.0360.177822.650724.181817.023
190.4128-0.1743-0.08380.47810.27220.1619-0.0072-0.04510.0825-0.05850.00740.154-0.1475-0.32390.00280.15290.10910.0080.23590.01850.166414.207318.290834.1082
200.6701-0.84010.05021.1674-0.1080.0216-0.00280.02770.2551-0.0525-0.0781-0.0864-0.2904-0.07420.06510.27170.0953-0.00190.1397-0.00060.201523.329330.679236.1414
210.4457-0.1420.10510.5627-0.28260.8564-0.0313-0.05310.11590.02520.02370.0512-0.2696-0.19080.00960.14520.02970.00660.0954-0.0180.107528.882519.862452.2158
221.1061-0.3875-0.24371.24150.18190.5812-0.0036-0.08460.19260.10120.0338-0.0513-0.26580.0597-0.01270.1701-0.0498-0.0030.0535-0.01660.122545.181220.849346.7897
230.00540.0247-0.00560.1931-0.05090.63050.0172-0.0444-0.00650.0372-0.0061-0.0281-0.00120.0039-0.01190.0668-0.0199-0.00580.065-0.00040.086939.59953.320851.3688
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 91 )
2X-RAY DIFFRACTION2chain 'A' and (resid 92 through 162 )
3X-RAY DIFFRACTION3chain 'A' and (resid 163 through 317 )
4X-RAY DIFFRACTION4chain 'A' and (resid 318 through 480 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 70 )
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 209 )
7X-RAY DIFFRACTION7chain 'B' and (resid 210 through 246 )
8X-RAY DIFFRACTION8chain 'B' and (resid 247 through 292 )
9X-RAY DIFFRACTION9chain 'B' and (resid 293 through 320 )
10X-RAY DIFFRACTION10chain 'B' and (resid 321 through 485 )
11X-RAY DIFFRACTION11chain 'B' and (resid 486 through 523 )
12X-RAY DIFFRACTION12chain 'C' and (resid 4 through 49 )
13X-RAY DIFFRACTION13chain 'C' and (resid 50 through 173 )
14X-RAY DIFFRACTION14chain 'C' and (resid 174 through 433 )
15X-RAY DIFFRACTION15chain 'C' and (resid 434 through 480 )
16X-RAY DIFFRACTION16chain 'D' and (resid 2 through 70 )
17X-RAY DIFFRACTION17chain 'D' and (resid 71 through 161 )
18X-RAY DIFFRACTION18chain 'D' and (resid 162 through 212 )
19X-RAY DIFFRACTION19chain 'D' and (resid 213 through 292 )
20X-RAY DIFFRACTION20chain 'D' and (resid 293 through 320 )
21X-RAY DIFFRACTION21chain 'D' and (resid 321 through 399 )
22X-RAY DIFFRACTION22chain 'D' and (resid 400 through 445 )
23X-RAY DIFFRACTION23chain 'D' and (resid 446 through 523 )

+
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