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- PDB-3ge6: CRYSTAL STRUCTURE OF A PUTATIVE NITROREDUCTASE IN COMPLEX WITH FM... -

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Basic information

Entry
Database: PDB / ID: 3ge6
TitleCRYSTAL STRUCTURE OF A PUTATIVE NITROREDUCTASE IN COMPLEX WITH FMN (EXIG_2970) FROM EXIGUOBACTERIUM SIBIRICUM 255-15 AT 1.85 A RESOLUTION
ComponentsNitroreductase
KeywordsOXIDOREDUCTASE / PUTATIVE NITROREDUCTASE IN COMPLEX WITH FMN / 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
FLAVIN MONONUCLEOTIDE / Nitroreductase
Similarity search - Component
Biological speciesExiguobacterium sibiricum 255-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative nitroreductase in complex with FMN (YP_001815433.1) from EXIGUOBACTERIUM SP. 255-15 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _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 / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id ..._pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nitroreductase
B: Nitroreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8864
Polymers47,9732
Non-polymers9132
Water8,269459
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-61 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.970, 81.300, 93.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 6 / Auth seq-ID: 3 - 211 / Label seq-ID: 4 - 212

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSTATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Nitroreductase


Mass: 23986.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum 255-15 (bacteria)
Gene: Exig_2970, YP_001815433.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: B1YG32
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O
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 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: 2.14 Å3/Da / Density % sol: 42.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2000M NH4H2PO3, 20.0000% PEG-3350, No Buffer pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97982
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 8, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97982 Å / Relative weight: 1
ReflectionResolution: 1.85→29.185 Å / Num. obs: 35856 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.089 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 6.79
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.85-1.920.5781.5131816970197.5
1.92-1.990.4342117106152198.5
1.99-2.080.3472.5128396732198.6
2.08-2.190.243.5127996696198.8
2.19-2.330.24.2131666874198.4
2.33-2.510.1495.4129836741199
2.51-2.760.116.9129586709199
2.76-3.160.0789.3131336770199
3.16-3.980.04414.2130756740198.7
3.98-29.1850.03318.1131196734198.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→29.185 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.919 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.135
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. A FLAVIN MONONUCLEOTIDE (FMN) MOLECULE IS MODELED INTO THE PUTATIVE ACTIVE SITE ON EACH SUBUNIT. THE FMN RESTRAINTS WERE CHANGED TO ALLOW BENDING OF THE ISOALLOXAZINE RING ALONG THE N5-N10 VIRTUAL AXIS RESULTING IN AN IMPROVED FIT BETWEEN THE FMN COORDINATES AND ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1791 5 %RANDOM
Rwork0.169 ---
obs0.171 35802 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.58 Å2 / Biso mean: 19.398 Å2 / Biso min: 6.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å20 Å2
2--0.02 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3246 0 62 459 3767
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223461
X-RAY DIFFRACTIONr_bond_other_d0.0010.022299
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9924709
X-RAY DIFFRACTIONr_angle_other_deg1.00435660
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8625435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52525.436149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8115611
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2611518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2531
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023847
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02627
X-RAY DIFFRACTIONr_nbd_refined0.2070.2695
X-RAY DIFFRACTIONr_nbd_other0.1970.22458
X-RAY DIFFRACTIONr_nbtor_refined0.1750.21681
X-RAY DIFFRACTIONr_nbtor_other0.0860.21673
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2328
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2980.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3310.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.215
X-RAY DIFFRACTIONr_mcbond_it2.13432246
X-RAY DIFFRACTIONr_mcbond_other0.5773862
X-RAY DIFFRACTIONr_mcangle_it2.82953494
X-RAY DIFFRACTIONr_scbond_it5.01581445
X-RAY DIFFRACTIONr_scangle_it7.131111215
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2673 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.415
LOOSE THERMAL1.9410
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 126 -
Rwork0.231 2415 -
all-2541 -
obs--98.68 %
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)
10.56940.03040.10430.33230.13920.3463-0.02320.02150.0042-0.01440.0317-0.0312-0.0110.0483-0.0085-0.02620.0031-0.0017-0.0294-0.0055-0.025625.923479.56755.1098
20.52270.0160.13150.60270.39150.632-0.0402-0.02710.0548-0.03030.00410.0759-0.0562-0.06360.0361-0.03180.0064-0.0038-0.0299-0.0021-0.030316.154988.58714.9824
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 211
2X-RAY DIFFRACTION2B2 - 211

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