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- PDB-2r01: Crystal structure of a putative fmn-dependent nitroreductase (ct0... -

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Basic information

Entry
Database: PDB / ID: 2r01
TitleCrystal structure of a putative fmn-dependent nitroreductase (ct0345) from chlorobium tepidum tls at 1.15 A resolution
ComponentsNitroreductase family protein
KeywordsOXIDOREDUCTASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding / metal ion binding
Similarity search - Function
putative fmn-dependent nitroreductase like fold / putative fmn-dependent nitroreductase like domains / Putative nitroreductase, C-terminal, bacterial / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / Single Sheet / 3-Layer(aba) Sandwich ...putative fmn-dependent nitroreductase like fold / putative fmn-dependent nitroreductase like domains / Putative nitroreductase, C-terminal, bacterial / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / Single Sheet / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / PHOSPHATE ION / Nitroreductase family protein
Similarity search - Component
Biological speciesChlorobium tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative FMN-dependent nitroreductase (NP_661249.1) from Chlorobium tepidum TLS at 1.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 1.4Jan 25, 2023Group: 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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 / _struct_conn.ptnr2_symmetry / _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
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE 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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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitroreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0565
Polymers23,4021
Non-polymers6534
Water4,089227
1
A: Nitroreductase family protein
hetero molecules

A: Nitroreductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,11110
Polymers46,8042
Non-polymers1,3078
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area8660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.030, 64.720, 48.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-389-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Nitroreductase family protein


Mass: 23402.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum TLS (bacteria) / Species: Chlorobaculum tepidum / Strain: TLS, DSM 12025 / Gene: NP_661249.1, CT0345 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8KFI1

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Non-polymers , 5 types, 231 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.02 Å3/Da / Density % sol: 39.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: NANODROP, 0.2M KH2PO4, 20.0% PEG 3350, No Buffer pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97949, 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 19, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979491
30.979221
ReflectionResolution: 1.15→28.49 Å / Num. obs: 66535 / % possible obs: 98.8 % / Redundancy: 3.14 % / Biso Wilson estimate: 7.078 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obs% possible all
1.15-1.190.3472.191906196.6
1.19-1.240.32.52124098.4
1.24-1.30.25332156198.7
1.3-1.360.2123.61796099.2
1.36-1.450.1684.52203599.3
1.45-1.560.1146.52055199.4
1.56-1.720.0769.32172799.6
1.72-1.970.04614.52149099.6
1.97-2.480.02822.72143999.3
2.48-28.490.01833.22176098.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.15→28.49 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 0.986 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.035 / ESU R Free: 0.033
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ONE FMN, ONE PHOSPHATE, ONE CALCIUM ION AND ONE ETHYLENE GLYCOL MOLECULES WERE MODELED. 5. RESIDUES 1 TO 12 ARE DISORDERED AND NOT MODELED IN THE STRUCTURE. 6. ELECTRON DENSITY NEAR RESIDUES 39 AND 56 IS UNMODELED, WHICH MAY BE THE FRACTION OF POLYETHYLENE GLYCOL.
RfactorNum. reflection% reflectionSelection details
Rfree0.165 3361 5.1 %RANDOM
Rwork0.148 ---
all0.149 ---
obs0.149 66493 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.107 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.53 Å2
Refinement stepCycle: LAST / Resolution: 1.15→28.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1478 0 41 227 1746
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221649
X-RAY DIFFRACTIONr_bond_other_d0.0020.021105
X-RAY DIFFRACTIONr_angle_refined_deg1.4542.0022268
X-RAY DIFFRACTIONr_angle_other_deg0.91632690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.81822.42466
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.30815264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5221518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021876
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02329
X-RAY DIFFRACTIONr_nbd_refined0.2220.3323
X-RAY DIFFRACTIONr_nbd_other0.1990.31250
X-RAY DIFFRACTIONr_nbtor_refined0.1730.5832
X-RAY DIFFRACTIONr_nbtor_other0.0870.5872
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.323
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.395
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.549
X-RAY DIFFRACTIONr_mcbond_it1.2431.51068
X-RAY DIFFRACTIONr_mcbond_other0.4781.5412
X-RAY DIFFRACTIONr_mcangle_it1.84621690
X-RAY DIFFRACTIONr_scbond_it2.3923693
X-RAY DIFFRACTIONr_scangle_it3.344.5578
X-RAY DIFFRACTIONr_rigid_bond_restr1.45633056
X-RAY DIFFRACTIONr_sphericity_free5.3873229
X-RAY DIFFRACTIONr_sphericity_bonded2.60832714
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 258 -
Rwork0.21 4501 -
obs-4759 97.14 %

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