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- PDB-3erp: Structure of IDP01002, a putative oxidoreductase from and essenti... -

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Basic information

Entry
Database: PDB / ID: 3erp
TitleStructure of IDP01002, a putative oxidoreductase from and essential gene of Salmonella typhimurium
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / FUNDED BY THE NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES OF NIH CONTRACT NUMBER HHSN272200700058C / predicted oxidoreductase / essential gene / Salmonella / molecular replacement / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


methylglyoxal catabolic process / nucleotide binding / metal ion binding
Similarity search - Function
Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CACODYLATE ION / Oxidoreductase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSinger, A.U. / Minasov, G. / Evdokimova, E. / Brunzelle, J.S. / Kudritska, M. / Edwards, A.M. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Appl.Environ.Microbiol. / Year: 2017
Title: Structural and biochemical studies of novel aldo-keto reductases for the biocatalytic conversion of 3-hydroxybutanal to 1,3-butanediol.
Authors: Kim, T. / Flick, R. / Brunzelle, J. / Singer, A. / Evdokimova, E. / Brown, G. / Joo, J.C. / Minasov, G.A. / Anderson, W.F. / Mahadevan, R. / Savchenko, A. / Yakunin, A.F.
History
DepositionOct 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_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_asym_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_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: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,15926
Polymers79,7242
Non-polymers1,43524
Water15,205844
1
A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules

B: Putative oxidoreductase
hetero molecules

B: Putative oxidoreductase
hetero molecules

B: Putative oxidoreductase
hetero molecules

B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)324,637104
Polymers318,8978
Non-polymers5,74096
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_444x-1/2,y-1/2,z-1/21
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
crystal symmetry operation7_544-y+1/2,x-1/2,z-1/21
crystal symmetry operation8_454y-1/2,-x+1/2,z-1/21
Buried area35410 Å2
ΔGint-507 kcal/mol
Surface area88530 Å2
MethodPISA
2
A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,86860
Polymers159,4484
Non-polymers3,42056
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area15860 Å2
ΔGint-246 kcal/mol
Surface area47470 Å2
MethodPISA
3
B: Putative oxidoreductase
hetero molecules

B: Putative oxidoreductase
hetero molecules

B: Putative oxidoreductase
hetero molecules

B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,76944
Polymers159,4484
Non-polymers2,32040
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area12440 Å2
ΔGint-272 kcal/mol
Surface area48170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.096, 127.096, 120.492
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-706-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative oxidoreductase


Mass: 39862.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: no TEV cleavage
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM2406 / Plasmid: p15TvLic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD(DE3) / References: UniProt: Q8ZNA1

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Non-polymers , 6 types, 868 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 844 / 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: 3.05 Å3/Da / Density % sol: 59.69 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6.5
Details: crystallized in 0.2 M Calcium Acetate, 9% PEG8000 and 0.1 M Sodium Cacodylate. Cryoprotected with 25% ethylene glycol., pH 6.5, EVAPORATION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 2, 2008 / Details: mirrors
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→30 Å / Num. all: 136598 / Num. obs: 132754 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 23.08
Reflection shellResolution: 1.55→1.61 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.62 / Num. unique all: 13638 / % possible all: 80.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0051refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1ZSX was used for MR on a crystal diffracting to 2.15 A on our RAXIS4 home source. The protein atoms from the model refined from that crystal were used for rigid body ...Starting model: PDB code 1ZSX was used for MR on a crystal diffracting to 2.15 A on our RAXIS4 home source. The protein atoms from the model refined from that crystal were used for rigid body refinement with the new data diffracting to 1.55 A.

1zsx


Resolution: 1.55→29.96 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.166 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.063 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17771 6743 5.1 %RANDOM. R-free set for the second crystal was imported from the first crystal and extended to 1.55 A
Rwork0.15342 ---
obs0.15465 125986 96.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.404 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å20 Å20 Å2
2---1.03 Å20 Å2
3---2.05 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 71 844 5835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0215784
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9657890
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4785742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25623.612299
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.137151000
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2841556
X-RAY DIFFRACTIONr_chiral_restr0.120.2807
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214659
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3091.53478
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.13725655
X-RAY DIFFRACTIONr_scbond_it3.31632306
X-RAY DIFFRACTIONr_scangle_it5.1914.52235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.554→1.594 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 410 -
Rwork0.258 7180 -
obs-7590 75.42 %

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