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- PDB-1r27: Crystal Structure of NarGH complex -

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Basic information

Entry
Database: PDB / ID: 1r27
TitleCrystal Structure of NarGH complex
Components(Respiratory nitrate reductase 1 ...) x 2
KeywordsOXIDOREDUCTASE / beta barrel / x-ray crystallography
Function / homology
Function and homology information


nitrate reductase (quinone) / NarGHI complex / nitrate metabolic process / nitrate reductase activity / anaerobic electron transport chain / anaerobic respiration / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding ...nitrate reductase (quinone) / NarGHI complex / nitrate metabolic process / nitrate reductase activity / anaerobic electron transport chain / anaerobic respiration / molybdopterin cofactor binding / 3 iron, 4 sulfur cluster binding / nitrate assimilation / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane / metal ion binding
Similarity search - Function
Nitrate reductase alpha subunit / nitrate reductase domain fold / nitrate reductase domain like / Nitrate reductase, alpha subunit / Nitrate reductase, beta subunit / Nitrate reductase, alpha subunit, N-terminal / Respiratory nitrate reductase beta, C-terminal / Nitrate reductase beta, C-terminal domain superfamily / Nitrate reductase, alpha subunit, N-terminal domain superfamily / Respiratory nitrate reductase alpha N-terminal ...Nitrate reductase alpha subunit / nitrate reductase domain fold / nitrate reductase domain like / Nitrate reductase, alpha subunit / Nitrate reductase, beta subunit / Nitrate reductase, alpha subunit, N-terminal / Respiratory nitrate reductase beta, C-terminal / Nitrate reductase beta, C-terminal domain superfamily / Nitrate reductase, alpha subunit, N-terminal domain superfamily / Respiratory nitrate reductase alpha N-terminal / Respiratory nitrate reductase beta C-terminal / Nitrate reductase alpha subunit-like, MopB domain / 4Fe-4S dicluster domain / Prokaryotic molybdopterin oxidoreductases signature 2. / Molybdopterin oxidoreductase, molybdopterin cofactor binding site / Prokaryotic molybdopterin oxidoreductases signature 1. / Prokaryotic molybdopterin oxidoreductases signature 3. / Molybdopterin oxidoreductase, prokaryotic, conserved site / Molybdopterin oxidoreductase Fe4S4 domain / Alpha-Beta Plaits - #20 / Molybdopterin dinucleotide-binding domain / Molydopterin dinucleotide binding domain / Barwin-like endoglucanases - #20 / Barwin-like endoglucanases / Aspartate decarboxylase-like domain superfamily / Molybdopterin oxidoreductase, 4Fe-4S domain / Prokaryotic molybdopterin oxidoreductases 4Fe-4S domain profile. / Molybdopterin oxidoreductase / Molybdopterin oxidoreductase / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / Alpha-Beta Plaits / Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / Chem-MGD / MOLYBDENUM ATOM / IRON/SULFUR CLUSTER / Respiratory nitrate reductase 1 alpha chain / Respiratory nitrate reductase 1 beta chain
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJormakka, M. / Richardson, D. / Byrne, B. / Iwata, S.
CitationJournal: Structure / Year: 2004
Title: Architecture of NarGH reveals a structural classification of Mo-bisMGD enzymes
Authors: Jormakka, M. / Richardson, D. / Byrne, B. / Iwata, S.
History
DepositionSep 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
C: Respiratory nitrate reductase 1 alpha chain
D: Respiratory nitrate reductase 1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,89320
Polymers397,3344
Non-polymers6,55916
Water41,8132321
1
A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,94710
Polymers198,6672
Non-polymers3,2798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14430 Å2
ΔGint-173 kcal/mol
Surface area48190 Å2
MethodPISA
2
C: Respiratory nitrate reductase 1 alpha chain
D: Respiratory nitrate reductase 1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,94710
Polymers198,6672
Non-polymers3,2798
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14490 Å2
ΔGint-173 kcal/mol
Surface area48100 Å2
MethodPISA
3
A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
hetero molecules

A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
hetero molecules

A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
hetero molecules

A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
hetero molecules

C: Respiratory nitrate reductase 1 alpha chain
D: Respiratory nitrate reductase 1 beta chain
hetero molecules

C: Respiratory nitrate reductase 1 alpha chain
D: Respiratory nitrate reductase 1 beta chain
hetero molecules

C: Respiratory nitrate reductase 1 alpha chain
D: Respiratory nitrate reductase 1 beta chain
hetero molecules

C: Respiratory nitrate reductase 1 alpha chain
D: Respiratory nitrate reductase 1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,615,57280
Polymers1,589,33716
Non-polymers26,23564
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation5_455x-1/2,y+1/2,z+1/21
crystal symmetry operation6_555-x+1/2,-y+1/2,z+1/21
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area145440 Å2
ΔGint-1460 kcal/mol
Surface area355360 Å2
MethodPISA
4
A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
hetero molecules

A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
hetero molecules

C: Respiratory nitrate reductase 1 alpha chain
D: Respiratory nitrate reductase 1 beta chain
hetero molecules

C: Respiratory nitrate reductase 1 alpha chain
D: Respiratory nitrate reductase 1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)807,78640
Polymers794,6688
Non-polymers13,11832
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation7_555-x+1/2,y+1/2,-z+1/21
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area71360 Å2
ΔGint-722 kcal/mol
Surface area179040 Å2
MethodPISA
5
A: Respiratory nitrate reductase 1 alpha chain
B: Respiratory nitrate reductase 1 beta chain
hetero molecules

C: Respiratory nitrate reductase 1 alpha chain
D: Respiratory nitrate reductase 1 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)403,89320
Polymers397,3344
Non-polymers6,55916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z+1/21
Buried area33640 Å2
ΔGint-350 kcal/mol
Surface area91560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.401, 298.300, 296.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

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Respiratory nitrate reductase 1 ... , 2 types, 4 molecules ACBD

#1: Protein Respiratory nitrate reductase 1 alpha chain / E.C.1.7.99.4 / nitrate reductase 1 alpha subunit


Mass: 140526.781 Da / Num. of mol.: 2 / Fragment: alpha chain / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: GL101 / References: UniProt: P09152, nitrate reductase
#2: Protein Respiratory nitrate reductase 1 beta chain / E.C.1.7.99.4 / nitrate reductase 1 beta subunit


Mass: 58140.312 Da / Num. of mol.: 2 / Fragment: beta chain / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: GL101 / References: UniProt: P11349, nitrate reductase

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Non-polymers , 5 types, 2337 molecules

#3: Chemical ChemComp-MO / MOLYBDENUM ATOM


Mass: 95.940 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mo
#4: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe4S4
#5: Chemical
ChemComp-MGD / 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE / MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE


Mass: 740.557 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H26N10O13P2S2
#6: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2321 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1500, NaCl, MgCl2, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
31 %OG1drop
49 %PEG15001reservoir
5100 mM1reservoirMgCl2
6100 mM1reservoirNaCl
75 %DMSO1reservoir
80.1 MHEPES1reservoirpH7.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12981
22981
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2911.7416, 1.7365, 1.4884
SYNCHROTRONESRF ID2920.9393
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDApr 13, 2003mirrors
ADSC QUANTUM 42CCDApr 13, 2003mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si111MADMx-ray1
2Si111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.74161
21.73651
31.48841
40.93931
ReflectionResolution: 2→39.86 Å / Num. obs: 332608 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.8 Å2
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. obs: 329239 / % possible obs: 88.3 % / Redundancy: 3.2 % / Num. measured all: 1060308 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 83.3 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
CNS1.1refinement
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2→39.86 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 8259633.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 10083 3 %RANDOM
Rwork0.204 ---
all0.205 ---
obs0.204 332608 88.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 61.0024 Å2 / ksol: 0.361625 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.44 Å20 Å20 Å2
2---6.49 Å20 Å2
3----1.95 Å2
Refine analyzeLuzzati coordinate error free: 0.29 Å / Luzzati sigma a free: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26742 0 268 2321 29331
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 1624 3.1 %
Rwork0.33 50304 -
obs--83.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PRO.PARPRO.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4WATER.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / % reflection Rfree: 1 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.8
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83
LS refinement shell
*PLUS
Lowest resolution: 2.09 Å / Rfactor Rwork: 0.335

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