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- PDB-4z0p: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r... -

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Basic information

Entry
Database: PDB / ID: 4z0p
TitleCrystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc02828 (SmGhrA) from Sinorhizobium meliloti in complex with NADPH and oxalate
ComponentsNAD-dependent dehydrogenase
KeywordsOXIDOREDUCTASE / New York Structural Genomics Research Consortium / NADPH / oxalate / PSI-Biology / NYSGRC / structural genomics
Function / homology
Function and homology information


NAD binding / oxidoreductase activity
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / OXALIC ACID / NAD-dependent dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSroka, P. / Gasiorowska, O.A. / Handing, K.B. / Shabalin, I.G. / Porebski, P.J. / Hillerich, B.S. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: Biochemistry / Year: 2018
Title: Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies.
Authors: Kutner, J. / Shabalin, I.G. / Matelska, D. / Handing, K.B. / Gasiorowska, O. / Sroka, P. / Gorna, M.W. / Ginalski, K. / Wozniak, K. / Minor, W.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Structure summary
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3May 16, 2018Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / exptl_crystal_grow / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.pdbx_ec / _exptl_crystal_grow.pdbx_details / _struct.pdbx_descriptor / _struct.title
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
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 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1768
Polymers34,7931
Non-polymers1,3837
Water7,728429
1
A: NAD-dependent dehydrogenase
hetero molecules

A: NAD-dependent dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,35216
Polymers69,5862
Non-polymers2,76714
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area9950 Å2
ΔGint-61 kcal/mol
Surface area24530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.099, 108.099, 80.226
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NAD-dependent dehydrogenase


Mass: 34792.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: R00152, SMc02828 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)-RIPL / References: UniProt: Q92T34, glyoxylate reductase (NADP+)

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Non-polymers , 6 types, 436 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-OXD / OXALIC ACID


Mass: 90.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2O4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 3.93 Å3/Da / Density % sol: 68.72 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7
Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, 5 mM NADPH, and 50 mM oxalic acid pH=7.0 were mixed with 0.2 ul of the MCSG Suite ...Details: 0.2 ul of 12 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP, 5 mM NADPH, and 50 mM oxalic acid pH=7.0 were mixed with 0.2 ul of the MCSG Suite 2 condition #28 (0.2M Ammonium Citrate Tribasic, anhydrous, 20%w/v PEG 3350 pH=7) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop. Before crystallization, the protein-ligand mixture was incubated with 1/15 v/v of 1 mg/ml rTEV solution at 289 K for 3 hours

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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: Nov 6, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 60027 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Rsym value: 0.074 / Χ2: 1.134 / Net I/av σ(I): 35.4 / Net I/σ(I): 8.3 / Num. measured all: 255923
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.7-1.736.70.8522.429010.7260.430.9380.793100
1.73-1.764.40.69728430.7690.3620.7890.77396.8
1.76-1.794.40.59228810.8290.3060.6690.84696.6
1.79-1.834.40.49928340.8810.260.5650.82996.4
1.83-1.874.50.41129140.9140.2120.4650.89996.4
1.87-1.914.40.31328060.9420.1620.3540.91696
1.91-1.964.50.26428600.950.1360.2990.96996
1.96-2.024.50.21528480.9690.1110.2430.99695.7
2.02-2.074.50.18428600.9740.0950.2081.0595.7
2.07-2.144.50.1528400.9820.0770.1691.07395.3
2.14-2.224.50.12228200.9870.0630.1381.12294.7
2.22-2.314.50.11328310.9890.0580.1271.17594.7
2.31-2.414.60.09828120.9910.0510.1111.21594.3
2.41-2.544.60.08128290.9930.0420.0921.21194
2.54-2.74.60.0727890.9940.0360.0791.32593.4
2.7-2.914.60.05827880.9960.030.0661.36993.1
2.91-3.24.70.04928000.9970.0250.0551.44192.2
3.2-3.664.60.04227690.9980.0210.0471.57391.6
3.66-4.614.70.03827560.9980.0190.0431.70290.2
4.61-504.60.03327660.9990.0170.0381.33486.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
HKL-3000data collection
BLU-MAXdata collection
HKL-3000phasing
MOLREPphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WEQ

4weq


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / WRfactor Rfree: 0.1486 / WRfactor Rwork: 0.1335 / FOM work R set: 0.9025 / SU B: 2.342 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0596 / SU Rfree: 0.0591 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1497 2954 4.9 %RANDOM
Rwork0.1344 ---
obs0.1351 56748 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.98 Å2 / Biso mean: 31.028 Å2 / Biso min: 16.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.2 Å20 Å2
2--0.39 Å2-0 Å2
3----1.28 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 83 429 2916
Biso mean--33.53 44.88 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192590
X-RAY DIFFRACTIONr_bond_other_d0.0020.022452
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.993538
X-RAY DIFFRACTIONr_angle_other_deg0.94635649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.645331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51823.491106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03415399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3761517
X-RAY DIFFRACTIONr_chiral_restr0.0880.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212898
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02570
X-RAY DIFFRACTIONr_mcbond_it3.1191.6311280
X-RAY DIFFRACTIONr_mcbond_other3.1161.6311279
X-RAY DIFFRACTIONr_mcangle_it3.8262.4271604
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 230 -
Rwork0.226 4165 -
all-4395 -
obs--100 %
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)
14.27182.995-1.20595.7863-3.33915.81360.00790.0349-0.2763-0.015-0.10130.04020.2946-0.19230.09340.11140.00660.04260.1014-0.01960.08938.771-31.419-39.064
21.2055-0.0833-0.56721.7448-0.06941.71450.09580.1309-0.04-0.1282-0.0535-0.0273-0.0694-0.0102-0.04230.02940.01070.01560.0630.03280.059244.162-27.403-42.082
311.4042-3.8313-9.487913.150811.427923.25840.25840.32480.6814-0.2540.5546-0.7068-0.69690.7441-0.81290.1459-0.05740.02660.16530.01790.140947.974-17.011-39.6
40.64430.3692-0.41470.444-0.34670.66360.04910.01940.0326-0.0202-0.0058-0.0323-0.04740.0369-0.04320.0421-0.03140.01130.0657-0.00230.076334.661-32.581-19.753
517.3089-3.5598-2.077310.33682.21076.7469-0.1018-0.23280.15730.3030.1885-0.53170.07280.4237-0.08670.1196-0.0291-0.02280.10060.05990.179923.327-60.06-4.369
61.05540.4315-0.20220.58230.14770.35710.0695-0.09860.05330.1046-0.0614-0.042-0.04810.0174-0.00810.0696-0.03590.0060.0816-0.01020.083826.218-33.351-5.627
76.8401-0.73010.01163.98320.26946.44920.01970.12750.4215-0.20040.0289-0.0465-0.280.0437-0.04860.0696-0.02390.01780.0856-0.00360.127621.599-29.927-9.392
823.239514.098-1.220413.3868-2.06663.16880.3748-0.61130.52520.3986-0.20860.4124-0.1462-0.0348-0.16630.163-0.03170.01050.1265-0.0560.166731.6-24.542-3.969
90.84192.9277-0.814210.4301-1.40939.8552-0.20690.11420.2608-1.03120.27780.9139-2.0932-0.835-0.07090.72470.121-0.1090.2708-0.00710.327732.223-16.414-8.087
100.97320.141-0.25570.4940.06131.10630.0341-0.12660.01870.0818-0.0295-0.1199-0.02640.1064-0.00470.0354-0.0434-0.0160.0806-0.00490.092140.703-35.092-6.391
111.2299-0.39710.01774.0925-2.98034.23230.01580.0430.0091-0.11460.0469-0.02360.1281-0.1623-0.06270.0453-0.04010.01820.1095-0.02820.116634.424-36.316-23.775
122.02010.18620.22420.3801-0.29594.55830.05960.02870.32060.02140.00980.0754-0.6024-0.2416-0.06930.13440.01680.04140.02280.01720.168937.929-14.384-30.113
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 19
2X-RAY DIFFRACTION2A20 - 62
3X-RAY DIFFRACTION3A63 - 68
4X-RAY DIFFRACTION4A69 - 124
5X-RAY DIFFRACTION5A125 - 130
6X-RAY DIFFRACTION6A131 - 155
7X-RAY DIFFRACTION7A156 - 163
8X-RAY DIFFRACTION8A164 - 169
9X-RAY DIFFRACTION9A170 - 176
10X-RAY DIFFRACTION10A177 - 272
11X-RAY DIFFRACTION11A273 - 296
12X-RAY DIFFRACTION12A297 - 319

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