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- PDB-4pmj: Crystal structure of a putative oxidoreductase from Sinorhizobium... -

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Basic information

Entry
Database: PDB / ID: 4pmj
TitleCrystal structure of a putative oxidoreductase from Sinorhizobium meliloti 1021 in complex with NADP
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / putative oxidoreductase / NADP / limited proteolysis.
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / oxidoreductase activity / nucleotide binding
Similarity search - Function
NADP-dependent oxidoreductase domain / Aldo-keto reductase / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsGasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Szlachta, K. / Zimmerman, M.D. / Hillerich, B.S. / Gizzi, A. / Toro, R. / Bonanno, J. / Seidel, R. ...Gasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Szlachta, K. / Zimmerman, M.D. / Hillerich, B.S. / Gizzi, A. / Toro, R. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIH-5U54GM094662-04 United States
CitationJournal: to be published
Title: Crystal structure of a putative oxidoreductase from Sinorhizobiummeliloti 1021 in complex with NADP
Authors: Gasiorowska, O.A. / Shabalin, I.G. / Handing, K.B. / Szlachta, K. / Zimmerman, M.D. / Hillerich, B.S. / Gizzi, A. / Toro, R. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W.
History
DepositionMay 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Data collection
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 13, 2022Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / diffrn_radiation_wavelength
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9213
Polymers31,0851
Non-polymers8352
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.324, 78.897, 79.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative oxidoreductase


Mass: 31085.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (bacteria) / Strain: 1021 / Gene: R02112, SMc01429 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL
References: UniProt: Q92NR7, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe protein was expressed with His tag and subjected to limited proteolysis by chymotrypsin

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-II condition #42 (1.1 M Ammonium Tartrate ...Details: 0.2 ul of 14 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of the MCSG-II condition #42 (1.1 M Ammonium Tartrate Dibasic pH 7.0) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization protein was incubated with 1/50 v/v of 2 mg/ml chymotrypsin solution at 289 K for 3 hours.
Temp details: Rigaku Gallery 700

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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: Mar 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 14760 / Num. obs: 14450 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/av σ(I): 11.4 / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 1.9 / % possible all: 85.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
HKL-3000data scaling
SHELXDEphasing
MLPHAREphasing
DMphasing
Cootmodel building
REFMAC5.8.0049refinement
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: SAD / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 12.06 / SU ML: 0.162 / SU R Cruickshank DPI: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.271 / ESU R Free: 0.201 / SU Rfree Cruickshank DPI: 0.2
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21676 731 5.1 %RANDOM
Rwork0.16725 ---
obs0.16977 13677 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.852 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0 Å2
2--1 Å2-0 Å2
3----1.02 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 54 115 2296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192233
X-RAY DIFFRACTIONr_bond_other_d0.0010.022128
X-RAY DIFFRACTIONr_angle_refined_deg1.6622.0063041
X-RAY DIFFRACTIONr_angle_other_deg0.94734877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.14522.91796
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.32815337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0631523
X-RAY DIFFRACTIONr_chiral_restr0.090.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02502
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_it0.7491.171125
X-RAY DIFFRACTIONr_mcbond_other0.7451.1691124
X-RAY DIFFRACTIONr_mcangle_it1.2571.7521405
X-RAY DIFFRACTIONr_mcangle_other1.2581.7531406
X-RAY DIFFRACTIONr_scbond_it1.3041.391108
X-RAY DIFFRACTIONr_scbond_other1.3011.391108
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0052.0231636
X-RAY DIFFRACTIONr_long_range_B_refined5.7210.3972562
X-RAY DIFFRACTIONr_long_range_B_other5.71910.4122563
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å
RfactorNum. reflection% reflection
Rfree0.235 41 5.1 %
Rwork0.254 854 -
obs--85.89 %
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)
112.82975.86088.89862.75664.627315.0278-0.29610.20920.8333-0.14810.07120.4564-10.20790.22490.12260.00850.09810.1695-0.04620.2894-11.0728.8714.897
22.0874-0.70990.36884.9306-1.97745.07540.041-0.0753-0.11430.0482-0.14-0.15170.30.32160.09910.02530.01220.00150.2772-0.01070.1447-3.601-7.09116.002
33.87821.32281.99461.95083.03724.73490.0307-0.1549-0.04560.0912-0.024-0.02140.1435-0.0269-0.00670.0092-0.01040.0110.2767-0.01560.1522-8.212-2.22915.244
44.0791-1.4199-0.34194.0803-1.13325.11640.0108-0.6165-0.09680.7674-0.03880.06890.4179-0.16860.02810.2689-0.085200.4594-0.03880.2243-12.623-8.87217.234
52.1343-0.1255-0.25954.35911.72371.7567-0.0666-0.1401-0.10310.05590.1217-0.0830.0879-0.0143-0.05510.0075-0.00460.01290.27570.02430.1419-16.356-13.3314.293
62.20240.1486-0.03670.58220.48182.5439-0.06280.0317-0.1693-0.02680.04510.11360.067-0.05120.01770.0063-0.001-0.00040.26490.00790.1828-17.529-13.5952.1
73.32430.7915-0.46891.0195-0.2171.2682-0.03730.17780.0803-0.08750.0712-0.0010.0297-0.0196-0.03390.00820.00240.00230.25990.01230.1166-9.487-5.654-5.791
85.9099-2.65773.51732.42-2.75283.77740.18270.19230.1076-0.09-0.187-0.03690.13940.2110.00430.00940.02550.01250.2503-0.02030.1506-1.616-1.745-1.509
92.44590.7257-0.69651.28080.5841.85220.1489-0.1350.26550.0195-0.0084-0.1717-0.23160.2481-0.14050.039-0.02370.0160.3192-0.01740.27287.1446.1956.244
102.88292.9836-5.55079.9998-11.524926.3777-0.52580.1417-0.3171-0.5007-0.0513-0.65570.59460.24080.57710.1096-0.03790.06660.23410.00750.12374.083-9.386-9.16
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 37
3X-RAY DIFFRACTION3A38 - 56
4X-RAY DIFFRACTION4A57 - 74
5X-RAY DIFFRACTION5A75 - 97
6X-RAY DIFFRACTION6A98 - 132
7X-RAY DIFFRACTION7A133 - 183
8X-RAY DIFFRACTION8A184 - 203
9X-RAY DIFFRACTION9A204 - 273
10X-RAY DIFFRACTION10A274 - 281

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