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- PDB-3eo7: Crystal structure of a putative nitroreductase (ava_2154) from an... -

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Basic information

Entry
Database: PDB / ID: 3eo7
TitleCrystal structure of a putative nitroreductase (ava_2154) from anabaena variabilis atcc 29413 at 1.80 A resolution
ComponentsPutative Nitroreductase
KeywordsFLAVOPROTEIN / 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
SagB-type dehydrogenase domain / NADH Oxidase / NADH Oxidase / Nitroreductase / Nitroreductase family / Nitroreductase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN MONONUCLEOTIDE / R-1,2-PROPANEDIOL / Nitroreductase domain-containing protein
Similarity search - Component
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative Nitroreductase (YP_322669.1) from ANABAENA VARIABILIS ATCC 29413 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,75919
Polymers58,3311
Non-polymers1,42818
Water9,152508
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.880, 93.880, 144.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative Nitroreductase


Mass: 58330.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Gene: YP_322669.1, Ava_2154 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3MB62

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Non-polymers , 6 types, 526 molecules

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


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PGR / R-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.16 Å3/Da / Density % sol: 61.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 40.0000% 1,2-propanediol, 0.0500M Ca(OAc)2, 0.1M Acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.918370,0.978985,0.979346
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2008 / Details: Vertical focusing mirror
RadiationMonochromator: Single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9789851
30.9793461
ReflectionResolution: 1.8→30.056 Å / Num. obs: 68777 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 20.106 Å2 / Rmerge F obs: 0.126 / Rmerge(I) obs: 0.068 / Net I/σ(I): 14.56
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.6182.34584212088197.9
1.86-1.940.4383.35401514207199.6
1.94-2.030.2955104913416199.7
2.03-2.130.2027.14731412428199.6
2.13-2.270.1529.35252813774199.7
2.27-2.440.11511.84899912852199.8
2.44-2.690.08714.85165513519199.9
2.69-3.070.05820.64940912957199.9
3.07-3.870.03630.95035213334199.8
3.87-30.060.026405127513327199.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→30.056 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 2.871 / SU ML: 0.048 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.08
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). 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. (3). ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. (4). THE DENSITIES OF RESIDUES 27-28, 59-63 AND 286-297 WERE POOR AND THEY WERE NOT MODELED. (5). THE DENSITIES OF RESIDUES 55-58 WERE POOR AND THEIR MODELS ARE NOT RELIABLE. (6). ONE FMN MONOMER WAS MODELED BASED ON THE PRESENCE OF CLEAR AND CONCLUSIVE ELECTRON DENSITY. (7). CA ION, CL IONS, ACETATE (ACT) IONS AND THE R-FORM (PGR) OF 1,2-PROPANE DIOL MOLECULES WERE MODELED BASED ON CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.163 3480 5.1 %RANDOM
Rwork0.137 ---
obs0.138 68745 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.19 Å2 / Biso mean: 23.88 Å2 / Biso min: 7.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å20 Å2
2--0.28 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.056 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3899 0 92 508 4499
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214257
X-RAY DIFFRACTIONr_bond_other_d0.0020.022794
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.9675817
X-RAY DIFFRACTIONr_angle_other_deg0.96736788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3285523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.46923.81210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.14715657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2281528
X-RAY DIFFRACTIONr_chiral_restr0.1030.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024885
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02898
X-RAY DIFFRACTIONr_nbd_refined0.2220.2837
X-RAY DIFFRACTIONr_nbd_other0.2050.23100
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22121
X-RAY DIFFRACTIONr_nbtor_other0.0860.22145
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2412
X-RAY DIFFRACTIONr_metal_ion_refined0.1920.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.273
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.213
X-RAY DIFFRACTIONr_mcbond_it2.00332667
X-RAY DIFFRACTIONr_mcbond_other0.47431020
X-RAY DIFFRACTIONr_mcangle_it2.8654148
X-RAY DIFFRACTIONr_scbond_it4.23981893
X-RAY DIFFRACTIONr_scangle_it5.846111669
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 257 -
Rwork0.181 4748 -
all-5005 -
obs--99.5 %
Refinement TLS params.Method: refined / Origin x: 49.3795 Å / Origin y: 32.4261 Å / Origin z: 2.3802 Å
111213212223313233
T-0.0401 Å2-0.0162 Å2-0.0062 Å2--0.0294 Å2-0.0056 Å2---0.0528 Å2
L0.5727 °20.228 °2-0.0518 °2-0.5441 °2-0.1309 °2--0.4842 °2
S-0.0045 Å °-0.0381 Å °0.0265 Å °-0.0085 Å °0.0046 Å °0.0192 Å °-0.0117 Å °-0.0489 Å °-0.0001 Å °

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