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- PDB-1hzv: DOMAIN SWING UPON HIS TO ALA MUTATION IN NITRITE REDUCTASE OF PSE... -

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Basic information

Entry
Database: PDB / ID: 1hzv
TitleDOMAIN SWING UPON HIS TO ALA MUTATION IN NITRITE REDUCTASE OF PSEUDOMONAS AERUGINOSA
ComponentsNITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / 8-bladed beta propeller
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase / Cytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome D1 heme domain / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / 8 Propeller / Methanol Dehydrogenase; Chain A / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. ...C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase / Cytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome D1 heme domain / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / 8 Propeller / Methanol Dehydrogenase; Chain A / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
HEME D / HEME C / NITRIC OXIDE / Nitrite reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.83 Å
AuthorsBrown, K. / Tegoni, M. / Cambillau, C.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Domain swing upon His to Ala mutation in nitrite reductase of Pseudomonas aeruginosa.
Authors: Brown, K. / Roig-Zamboni, V. / Cutruzzola, F. / Arese, M. / Sun, W. / Brunori, M. / Cambillau, C. / Tegoni, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: The Nitrite Reductase from Pseudomonas aeruginosa: Essential Role of Two Active-site Histidines in the Catalytic and Structural Properties.
Authors: Cutruzzola, F. / Brown, K. / Wilson, E.K. / Bellelli, A. / Arese, M. / Tegoni, M. / Cambillau, C. / Brunori, M.
History
DepositionJan 26, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_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_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5534
Polymers60,1921
Non-polymers1,3613
Water5,945330
1
A: NITRITE REDUCTASE
hetero molecules

A: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,1068
Polymers120,3842
Non-polymers2,7226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)94.744, 94.744, 159.901
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-709-

HOH

21A-716-

HOH

31A-865-

HOH

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Components

#1: Protein NITRITE REDUCTASE


Mass: 60191.988 Da / Num. of mol.: 1 / Mutation: H369A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: NIRS / Plasmid: PNM185 (PEMBL18NR) / Production host: Pseudomonas putida (bacteria) / Strain (production host): PAW340 / References: UniProt: P24474, EC: 1.9.3.2
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-DHE / HEME D


Mass: 712.484 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O10
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG6000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111.5 %PEG60001reservoir
20.2 Mimidazole malate1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM1411.7389,1.7401,0.9918
SYNCHROTRONESRF ID14-220.9326
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDMar 25, 2000mirror
ADSC QUANTUM 42CCDApr 12, 2000mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1si 111MADMx-ray1
2si 111SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.73891
21.74011
30.99181
40.93261
ReflectionResolution: 2.8→28 Å / Num. all: 17823 / Num. obs: 17423 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 79 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 13.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1718 / Rsym value: 0.36 / % possible all: 99.8
Reflection shell
*PLUS
% possible obs: 99.8 % / Rmerge(I) obs: 0.36

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.83→19.91 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1703480.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.296 841 4.8 %random
Rwork0.282 ---
all0.286 17823 --
obs0.286 17382 96.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.0148 Å2 / ksol: 0.232413 e/Å3
Displacement parametersBiso mean: 106.9 Å2
Baniso -1Baniso -2Baniso -3
1-7.23 Å20 Å20 Å2
2--7.23 Å20 Å2
3----14.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.55 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.7 Å
Refinement stepCycle: LAST / Resolution: 2.83→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4032 0 94 330 4456
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.021
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d2.39
X-RAY DIFFRACTIONc_mcbond_it2.521.5
X-RAY DIFFRACTIONc_mcangle_it4.182
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it3.232.5
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.055 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.538 94 3.9 %
Rwork0.457 2290 -
obs-1659 79.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PAR_VILMOS.HEMTOP_VILMOS.HEM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.8 % / Rfactor obs: 0.282
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 106.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg2.39
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.538 / % reflection Rfree: 3.9 % / Rfactor Rwork: 0.457

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