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- PDB-4xpi: Fe protein independent substrate reduction by nitrogenase variant... -

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Basic information

Entry
Database: PDB / ID: 4xpi
TitleFe protein independent substrate reduction by nitrogenase variants altered in intramolecular electron transfer
Components(Nitrogenase molybdenum-iron protein ...) x 2
KeywordsOXIDOREDUCTASE / NITROGEN FIXATION / MoFe protein / nitrogenase / proton reduction / nitrogen / acetylene / hydride reduction / ATP-binding / Iron / Iron-sulfur / Metal-binding / Nucleotide-binding / Molybdenum
Function / homology
Function and homology information


molybdenum-iron nitrogenase complex / nitrogenase / nitrogenase activity / nitrogen fixation / iron-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 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 Molybdenum-iron Protein, subunit B, domain 4 / Nitrogenase Molybdenum-iron Protein, subunit B; domain 4 / 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 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE(8)-S(7) CLUSTER, OXIDIZED / 3-HYDROXY-3-CARBOXY-ADIPIC ACID / Chem-ICS / 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: 1.97 Å
AuthorsDanyal, K. / Rasmusen, A.J. / Keable, S.M. / Shaw, S. / Zadvornyy, O. / Duval, S. / Dean, D.R. / Raugei, S. / Peters, J.W. / Seefeldt, L.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1330807 United States
CitationJournal: Biochemistry / Year: 2015
Title: Fe protein-independent substrate reduction by nitrogenase MoFe protein variants.
Authors: Danyal, K. / Rasmussen, A.J. / Keable, S.M. / Inglet, B.S. / Shaw, S. / Zadvornyy, O.A. / Duval, S. / Dean, D.R. / Raugei, S. / Peters, J.W. / Seefeldt, L.C.
History
DepositionJan 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Advisory / Author supporting evidence / Derived calculations
Category: pdbx_audit_support / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 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 / 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 / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,05629
Polymers229,0214
Non-polymers5,03525
Water16,592921
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area34620 Å2
ΔGint-189 kcal/mol
Surface area58430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.804, 130.830, 108.110
Angle α, β, γ (deg.)90.00, 111.14, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A5 - 480
2114C5 - 480
1124B2 - 527
2124D2 - 527

NCS ensembles :
ID
1
2

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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: 55130.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifD / Production host: Azotobacter vinelandii (bacteria) / Strain (production host): DJ939 / References: UniProt: P07328, nitrogenase
#2: Protein Nitrogenase molybdenum-iron protein beta chain / Dinitrogenase / Nitrogenase component I


Mass: 59379.652 Da / Num. of mol.: 2 / Mutation: Y98H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (bacteria) / Gene: nifK / Production host: Azotobacter vinelandii (bacteria) / Strain (production host): DJ939 / References: UniProt: P07329, nitrogenase

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Non-polymers , 7 types, 946 molecules

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


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


Mass: 787.451 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CFe7MoS9
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-1CL / FE(8)-S(7) CLUSTER, OXIDIZED


Mass: 671.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe8S7
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 8
Details: 30% PEG 4000, 100mM Tris-HCl pH 8.0, 170-190mM Sodium molybdate and 1mM Dithionite, LIQUID DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.97→35.8 Å / Num. obs: 141514 / % possible obs: 96.39 % / Redundancy: 3.5 % / Net I/σ(I): 2.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U7Q

3u7q


Resolution: 1.97→35 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.25 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26359 7087 5 %RANDOM
Rwork0.21303 ---
obs0.21557 134339 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.796 Å2
Baniso -1Baniso -2Baniso -3
1-3.66 Å20 Å20.5 Å2
2---0.91 Å20 Å2
3----2.39 Å2
Refinement stepCycle: LAST / Resolution: 1.97→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15937 0 202 921 17060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0216562
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211471
X-RAY DIFFRACTIONr_angle_refined_deg2.9221.9722448
X-RAY DIFFRACTIONr_angle_other_deg1.404327919
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73852005
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.53124.121762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.534152884
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5251592
X-RAY DIFFRACTIONr_chiral_restr0.2730.22388
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02118192
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023394
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A6480MEDIUM POSITIONAL0.180.5
1A6480MEDIUM THERMAL2.232
2B7101MEDIUM POSITIONAL0.120.5
2B7101MEDIUM THERMAL1.512
LS refinement shellResolution: 1.974→2.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 421 -
Rwork0.274 7855 -
obs--77.48 %
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)
115.380730.753-0.336961.4914-0.67440.0077-0.34880.58110.34950.14750.77090.7054-0.0106-0.0166-0.42210.34190.20710.0690.1978-0.09030.4125-36.386428.818459.1118
20.74271.1005-0.66531.641-0.84463.23670.4002-0.07310.06430.6302-0.18290.1118-0.5681-0.6211-0.21730.33140.07590.09080.3578-0.0620.2114-38.245515.285264.3754
30.26030.0174-0.12120.4850.04070.60780.0229-0.0707-0.05890.1473-0.0788-0.00320.0964-0.01340.05590.0989-0.0425-0.04720.21420.04790.1997-13.6008-11.449359.0304
40.33680.17670.0350.4226-0.07890.64590.0715-0.07250.01350.1692-0.12780.0429-0.19450.00280.05620.1384-0.0462-0.05030.1927-0.00060.1593-11.77412.300460.6502
515.3695-9.005426.88455.2772-15.751847.0271-0.9071-1.6057-0.08770.58141.00820.047-1.6729-2.7986-0.10110.61710.2650.05350.3601-0.15050.2146-36.692421.958826.4688
60.38310.1074-0.15350.09080.00850.7820.0346-0.04580.00050.0637-0.1040.00050.0361-0.08180.06940.0732-0.0464-0.02620.20320.01420.2056-19.8039-6.042251.4094
70.45730.0397-0.07850.12540.33981.01520.01510.0510.06570.043-0.10930.02140.1031-0.31790.09420.0261-0.0669-0.03430.357-0.02370.2545-38.5225-12.901835.112
80.44230.3448-0.14180.2775-0.18790.9277-0.12530.0487-0.01-0.12090.05630.00460.2254-0.28020.0690.0957-0.0754-0.04710.2615-0.02180.2028-31.1751-15.157324.5437
90.3190.117-0.00340.4111-0.1150.8759-0.05330.0184-0.0719-0.0233-0.0293-0.04830.14070.00050.08260.0719-0.0007-0.0180.17870.01530.2258-10.5568-15.190431.6057
101.7071-0.32150.52352.4246-0.88390.42570.01380.0095-0.0142-0.0328-0.0688-0.07850.01890.05890.0550.07850.02070.02070.26330.06690.24286.3857-1.648418.9091
111.19390.1278-1.34351.3081-1.24372.4498-0.25160.26680.0233-0.6911-0.0744-0.39850.8318-0.21930.3260.56-0.03320.17380.1595-0.00780.1588-3.2814-15.7386-22.1518
120.16980.1003-0.11890.38430.01180.9789-0.0130.00420.0559-0.1311-0.1447-0.1025-0.07580.16420.15780.0869-0.0097-0.00450.23230.1130.255210.625712.8657-1.1109
131.1257-0.40771.03730.8274-0.99241.6446-0.1489-0.05160.3046-0.3933-0.3608-0.31240.18250.31160.50970.38050.21230.0520.3110.18520.239821.94887.4611-7.2725
140.28810.0556-0.28560.303-0.44490.8924-0.1101-0.0563-0.025-0.2622-0.1724-0.12380.43610.20310.28260.23890.140.12150.20780.07590.254911.9041-15.333-1.5453
1531.04431.1463-8.62810.72471.36076.54330.0560.3519-0.56390.2175-0.0154-0.08410.5638-0.1711-0.04060.331-0.2149-0.07850.1901-0.01460.2224-21.6473-20.61957.344
160.146-0.0358-0.15520.1166-0.2551.2604-0.00920.0473-0.0152-0.069-0.1403-0.04690.02480.21160.14950.13750.04490.00250.22140.09990.21565.64775.11876.3977
170.471-0.3169-0.23430.22980.07830.65730.04170.1396-0.0015-0.0529-0.08970.0065-0.0166-0.25790.0480.11990.026-0.08210.28860.00710.1625-20.48479.9922-7.4829
180.3464-0.1590.0780.2507-0.23661.02190.02520.03630.04410.0563-0.01940.0315-0.3137-0.1842-0.00580.12650.0859-0.04990.22580.00930.2154-24.541518.25613.8996
190.352-0.0083-0.14570.367-0.20090.9074-0.029-0.03460.01470.0255-0.0395-0.0304-0.19640.02610.06850.0918-0.0157-0.06570.16450.01760.1901-5.726815.103220.3335
201.56320.6084-0.02851.5865-0.49430.198-0.01180.0123-0.01280.082-0.038-0.0185-0.08250.07070.04980.1548-0.0463-0.07280.23170.04480.1817-2.12671.869740.7948
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 7
2X-RAY DIFFRACTION2A8 - 44
3X-RAY DIFFRACTION3A45 - 171
4X-RAY DIFFRACTION4A172 - 477
5X-RAY DIFFRACTION5A478 - 481
6X-RAY DIFFRACTION6B2 - 174
7X-RAY DIFFRACTION7B175 - 262
8X-RAY DIFFRACTION8B263 - 366
9X-RAY DIFFRACTION9B367 - 502
10X-RAY DIFFRACTION10B503 - 523
11X-RAY DIFFRACTION11C3 - 51
12X-RAY DIFFRACTION12C52 - 172
13X-RAY DIFFRACTION13C173 - 218
14X-RAY DIFFRACTION14C219 - 471
15X-RAY DIFFRACTION15C472 - 480
16X-RAY DIFFRACTION16D2 - 124
17X-RAY DIFFRACTION17D125 - 278
18X-RAY DIFFRACTION18D279 - 379
19X-RAY DIFFRACTION19D380 - 502
20X-RAY DIFFRACTION20D503 - 523

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