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- PDB-3hj9: Crystal structure of a putative nitroreductase (reut_a1228) from ... -

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Basic information

Entry
Database: PDB / ID: 3hj9
TitleCrystal structure of a putative nitroreductase (reut_a1228) from ralstonia eutropha jmp134 at 2.00 A resolution
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / Nitroreductase domain-containing protein
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of oxidoreductase (YP_295443.1) from RALSTONIA EUTROPHA JMP134 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8167
Polymers49,7022
Non-polymers1,1145
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-54 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.865, 78.865, 136.555
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Oxidoreductase /


Mass: 24851.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / Gene: Reut_A1228, YP_295443.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q472T4

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Non-polymers , 5 types, 292 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.47 Å3/Da / Density % sol: 50.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1860M magnesium acetate, 13.6000% polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97837
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 19, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978371
ReflectionResolution: 2→68.359 Å / Num. obs: 33910 / % possible obs: 99.8 % / Redundancy: 5.2 % / Biso Wilson estimate: 22.833 Å2 / Rmerge(I) obs: 0.105 / Rsym value: 0.105 / Net I/σ(I): 5.925
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.113.70.4511.41782748240.45198.8
2.11-2.245.40.36622474746150.366100
2.24-2.395.60.2972.42446143990.297100
2.39-2.585.60.2193.32250440410.219100
2.58-2.835.60.1744.12093037670.174100
2.83-3.165.50.11761891834090.117100
3.16-3.655.50.0748.71662330160.074100
3.65-4.475.50.0639.81412325770.063100
4.47-6.325.40.0512.71106420610.05100
6.32-68.3650.04114599512010.04199.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.25data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→68.359 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 7.948 / SU ML: 0.104 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.143
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ACETATE ION (ACT), MG ION, AND 2-METHYL-2,4-PENTANEDIOL (MPD) MOLECULE FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTIONS ARE MODELED. 5. ONE FLAVIN MONONUCLEOTIDE (FMN) MOLECULE IS MODELED IN EACH CHAIN BASED ON THE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1715 5.1 %RANDOM
Rwork0.174 ---
obs0.176 33851 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 51.15 Å2 / Biso mean: 22.434 Å2 / Biso min: 9.04 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å2-0.84 Å20 Å2
2---1.67 Å20 Å2
3---2.51 Å2
Refinement stepCycle: LAST / Resolution: 2→68.359 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 75 287 3593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223463
X-RAY DIFFRACTIONr_bond_other_d0.0030.022354
X-RAY DIFFRACTIONr_angle_refined_deg1.7362.0094743
X-RAY DIFFRACTIONr_angle_other_deg1.37835734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0775449
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.93322.662139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60215545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8491531
X-RAY DIFFRACTIONr_chiral_restr0.1040.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213863
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02683
X-RAY DIFFRACTIONr_mcbond_it1.16622163
X-RAY DIFFRACTIONr_mcbond_other0.262863
X-RAY DIFFRACTIONr_mcangle_it1.89933470
X-RAY DIFFRACTIONr_scbond_it1.25121300
X-RAY DIFFRACTIONr_scangle_it1.91531260
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 142 -
Rwork0.247 2299 -
all-2441 -
obs--97.13 %
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)
12.2017-0.1332-0.51321.879-0.09372.0064-0.04020.10880.0675-0.11790.0452-0.0585-0.05930.0617-0.0050.0583-0.01830.00020.01480.00360.0044-20.112652.00917.0021
21.62640.5239-0.42822.4878-0.12211.92090.0492-0.1613-0.10550.183-0.00180.02590.1599-0.0925-0.04740.0618-0.0207-0.00120.05180.00910.0146-32.899841.534125.6409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 216
2X-RAY DIFFRACTION2B7 - 216

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