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- PDB-3l6d: Crystal structure of putative oxidoreductase from Pseudomonas put... -

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Basic information

Entry
Database: PDB / ID: 3l6d
TitleCrystal structure of putative oxidoreductase from Pseudomonas putida KT2440
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


organic acid catabolic process / NADP binding / oxidoreductase activity
Similarity search - Function
: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily ...: / NADPH-dependent reductive aminase-like, C-terminal domain / : / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMalashkevich, V.N. / Patskovsky, Y. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
Citation
Journal: To be Published
Title: Crystal structure of putative oxidoreductase from Pseudomonas putida KT2440
Authors: Malashkevich, V.N. / Patskovsky, Y. / Toro, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
#1: Journal: J.MOL.CATAL., B ENZYM. / Year: 2015
Title: Characterization of three novel enzymes with imine reductase activity
Authors: Gand, M. / Muller, H. / Wardenga, R. / Hohne, M.
History
DepositionDec 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 24, 2012Group: Database references / Structure summary
Revision 1.3May 20, 2015Group: Database references
Revision 1.4Nov 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 1.5Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.6Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
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
Revision 1.7Oct 30, 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: Putative oxidoreductase
B: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)66,7532
Polymers66,7532
Non-polymers00
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8770 Å2
ΔGint-84 kcal/mol
Surface area24300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.342, 37.647, 104.252
Angle α, β, γ (deg.)90.000, 93.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A-99999 - 99999
2111B-99999 - 99999

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Components

#1: Protein Putative oxidoreductase


Mass: 33376.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: NP_744942.1, PP2798 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: Q88J51
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM Hepes pH 7.5, 25% PEG 3350, 200mM Magnesium Chloride hexahydrate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.76→50 Å / Num. obs: 51537 / % possible obs: 96.3 % / Redundancy: 3 % / Rmerge(I) obs: 0.082 / Χ2: 0.648 / Net I/σ(I): 5
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.76-1.822.7115770.23189.5
1.82-1.93126370.251197.30.765
1.9-1.982.9125610.609197.80.629
1.98-2.093.1128220.328199.90.288
2.09-2.223.2129550.3811000.2
2.22-2.392.8115170.7189.70.156
2.39-2.633.2128350.60111000.108
2.63-3.013.2128960.83111000.082
3.01-3.793123481.365195.40.073
3.79-503120611.149193.80.054

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.222 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.786 / SU B: 9.393 / SU ML: 0.122 / SU R Cruickshank DPI: 0.162 / SU Rfree: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2610 5.1 %RANDOM
Rwork0.208 ---
obs0.211 51537 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 80.47 Å2 / Biso mean: 31.431 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.1 Å2
2--0.25 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4438 0 0 314 4752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0214565
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.9256202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4585594
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56223.221208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.29815700
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.031532
X-RAY DIFFRACTIONr_chiral_restr0.1070.2705
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023510
X-RAY DIFFRACTIONr_mcbond_it1.3023.52919
X-RAY DIFFRACTIONr_mcangle_it3.963504629
X-RAY DIFFRACTIONr_scbond_it8.571501646
X-RAY DIFFRACTIONr_scangle_it1.5554.51570
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2181 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
TIGHT POSITIONAL0.635
TIGHT THERMAL2.6410
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.509 186 -
Rwork0.503 3278 -
all-3464 -
obs--91.35 %
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)
11.3130.39320.47750.22560.31260.65380.0668-0.1367-0.03610.0129-0.0655-0.02140.1269-0.0281-0.00120.07330.02150.00160.03840.02140.068732.746316.439333.0506
21.6755-0.20060.47010.2626-0.2520.63730.0715-0.0282-0.04360.0233-0.03520.03220.06610.04-0.03630.0885-0.01040.01340.0085-0.00820.06555.379914.960117.8994
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 294
2X-RAY DIFFRACTION2B2 - 296

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