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- PDB-3ip3: Structure of putative oxidoreductase (TM_0425) from Thermotoga ma... -

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Basic information

Entry
Database: PDB / ID: 3ip3
TitleStructure of putative oxidoreductase (TM_0425) from Thermotoga maritima
ComponentsOxidoreductase, putative
KeywordsOXIDOREDUCTASE / structural genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


: / : / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...: / : / GFO/IDH/MocA C-terminal domain / Oxidoreductase family, C-terminal alpha/beta domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Oxidoreductase, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.14 Å
AuthorsRamagopal, U.A. / Morano, C. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of putative oxidoreductase (TM_0425) from Thermotoga maritima
Authors: Ramagopal, U.A. / Morano, C. / Burley, S.K. / Almo, S.C.
History
DepositionAug 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, putative
B: Oxidoreductase, putative
C: Oxidoreductase, putative
D: Oxidoreductase, putative
E: Oxidoreductase, putative
F: Oxidoreductase, putative
G: Oxidoreductase, putative
H: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,21313
Polymers310,7338
Non-polymers4805
Water4,756264
1
A: Oxidoreductase, putative
B: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,9715
Polymers77,6832
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-73 kcal/mol
Surface area25570 Å2
MethodPISA
2
C: Oxidoreductase, putative
D: Oxidoreductase, putative


Theoretical massNumber of molelcules
Total (without water)77,6832
Polymers77,6832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-26 kcal/mol
Surface area25800 Å2
MethodPISA
3
E: Oxidoreductase, putative
F: Oxidoreductase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8754
Polymers77,6832
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-57 kcal/mol
Surface area25730 Å2
MethodPISA
4
G: Oxidoreductase, putative
H: Oxidoreductase, putative


Theoretical massNumber of molelcules
Total (without water)77,6832
Polymers77,6832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-25 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.009, 94.181, 142.852
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxidoreductase, putative


Mass: 38841.605 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM_0425 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYQ6
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M Bis-Tris pH 5.5, 25% PEG 3350, 0.2M NaCl2, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 170354 / % possible obs: 99.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.081 / Χ2: 1.071 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.14-2.234.80.674168870.95299.3
2.23-2.324.80.498169080.97299.5
2.32-2.424.90.361169710.95499.7
2.42-2.554.90.274169440.96399.7
2.55-2.714.90.197170040.99599.8
2.71-2.924.90.134169820.9899.8
2.92-3.2150.095170671.01399.9
3.21-3.685.20.073171151.066100
3.68-4.635.20.062171751.2100
4.63-505.10.055173011.56799.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.14→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.824 / SU B: 5.583 / SU ML: 0.145 / SU R Cruickshank DPI: 0.236 / SU Rfree: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.242 8541 5 %RANDOM
Rwork0.204 ---
obs0.206 170309 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 122.68 Å2 / Biso mean: 52.761 Å2 / Biso min: 22.47 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å21.03 Å2
2--0.92 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 2.14→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21126 0 25 264 21415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02221596
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.96129162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63752625
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.31323.635982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.512153975
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.51615152
X-RAY DIFFRACTIONr_chiral_restr0.0880.23252
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116026
X-RAY DIFFRACTIONr_mcbond_it0.6761.513050
X-RAY DIFFRACTIONr_mcangle_it1.276221170
X-RAY DIFFRACTIONr_scbond_it1.83538546
X-RAY DIFFRACTIONr_scangle_it3.0844.57991
LS refinement shellResolution: 2.14→2.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 585 -
Rwork0.282 11495 -
all-12080 -
obs--96.29 %

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