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- PDB-5v72: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r... -

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Basic information

Entry
Database: PDB / ID: 5v72
TitleCrystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with citrate
ComponentsNADPH-dependent glyoxylate/hydroxypyruvate reductase
KeywordsOXIDOREDUCTASE / NADPH-dependent glyoxylate/hydroxypyruvate reductase / NADP / NYSGRC / Sinorhizobium meliloti / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / 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
CITRIC ACID / 2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsShabalin, I.G. / Handing, K.B. / Gasiorowska, O.A. / Cooper, D.R. / Matelska, D. / Bonanno, J. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094662 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM117080 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HG008424 United States
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 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 16, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
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
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Oct 4, 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 / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADPH-dependent glyoxylate/hydroxypyruvate reductase
B: NADPH-dependent glyoxylate/hydroxypyruvate reductase
C: NADPH-dependent glyoxylate/hydroxypyruvate reductase
D: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,62715
Polymers137,0864
Non-polymers54111
Water20,7351151
1
A: NADPH-dependent glyoxylate/hydroxypyruvate reductase
C: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9679
Polymers68,5432
Non-polymers4247
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-79 kcal/mol
Surface area25420 Å2
MethodPISA
2
B: NADPH-dependent glyoxylate/hydroxypyruvate reductase
D: NADPH-dependent glyoxylate/hydroxypyruvate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6606
Polymers68,5432
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-68 kcal/mol
Surface area24560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.188, 157.926, 64.719
Angle α, β, γ (deg.)90.000, 110.740, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA3 - 3163 - 316
21ARGARGBB3 - 3163 - 316
12GLNGLNAA3 - 3213 - 321
22GLNGLNCC3 - 3213 - 321
13ARGARGAA3 - 3183 - 318
23ARGARGDD3 - 3183 - 318
14ARGARGBB3 - 3163 - 316
24ARGARGCC3 - 3163 - 316
15ARGARGBB3 - 3173 - 317
25ARGARGDD3 - 3173 - 317
16ALAALACC3 - 3193 - 319
26ALAALADD3 - 3193 - 319

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NADPH-dependent glyoxylate/hydroxypyruvate reductase


Mass: 34271.418 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: His-tag-labelled protein was subjected to limited proteolysis by chymotrypsin immediately prior to crystallization.
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc04462 / Plasmid: pSGC-His / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)-RIPL / References: UniProt: Q92LZ4, hydroxypyruvate reductase

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Non-polymers , 5 types, 1162 molecules

#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1151 / 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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 uL of 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP + 0.2 uL MCSG Suite II condition #9 (0.1 M sodium citrate, pH 5.0, 20% ...Details: 0.2 uL of 13 mg/mL protein in 20 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 0.1% sodium azide, 0.5 mM TCEP + 0.2 uL MCSG Suite II condition #9 (0.1 M sodium citrate, pH 5.0, 20% w/v PEG6000), equilibrated against 1.5 M sodium chloride in a 96-well 3-drop crystallization plate (Swissci), incubated with 1/50 v/v 2 mg/mL chymotrypsin solution at 289 K for 3 hours prior to crystallization

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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: Jul 25, 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: 2.1→50 Å / Num. obs: 68211 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.062 / Rrim(I) all: 0.115 / Rsym value: 0.096 / Χ2: 1.096 / Net I/av σ(I): 12.5 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allRsym valueΧ2% possible all
2.1-2.143.20.4312.334450.8340.2790.5150.4310.81399.1
2.14-2.183.20.3842.60.850.250.460.3840.82399.9
5.7-503.10.0610.9890.040.0730.0611.56389.8

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
REFMAC5.8.0158refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5UOG

5uog


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.266 / SU ML: 0.143 / SU R Cruickshank DPI: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.241 / ESU R Free: 0.177
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.204 3350 4.9 %RANDOM
Rwork0.1642 ---
obs0.1662 64518 98.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.14 Å2 / Biso mean: 35.344 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å2-0 Å2-1.07 Å2
2--2.13 Å20 Å2
3----1.76 Å2
Refinement stepCycle: final / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9315 0 28 1151 10494
Biso mean--38.11 39.86 -
Num. residues----1264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.029542
X-RAY DIFFRACTIONr_bond_other_d0.0020.029289
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.98213016
X-RAY DIFFRACTIONr_angle_other_deg0.978321288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90451263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.34722.638345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.873151444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1751587
X-RAY DIFFRACTIONr_chiral_restr0.0820.21606
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021889
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A182600.07
12B182600.07
21A187100.08
22C187100.08
31A183700.07
32D183700.07
41B186260.05
42C186260.05
51B185400.05
52D185400.05
61C188020.06
62D188020.06
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 262 -
Rwork0.25 4825 -
all-5087 -
obs--99.51 %
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)
11.7699-0.41290.99761.622-0.06941.9184-0.0443-0.16690.05650.12730.0426-0.0063-0.0834-0.11360.00170.19920.0367-0.02530.06990.00840.082630.57580.00389.12
20.03920.03340.16360.2849-0.06030.9096-0.00420.0093-0.0037-0.01080.013-0.0175-0.0330.1047-0.00880.1750.027-0.01850.08820.00450.084135.24183.67656.842
35.4681-1.45242.11083.69290.73376.2303-0.0373-0.1641-0.16690.22830.0546-0.43980.47530.3456-0.01720.16280.0433-0.01810.2409-0.01570.164952.64480.62756.648
47.3428-1.96354.94115.69953.001919.14190.0106-0.2490.26130.22860.0952-0.36040.10590.0601-0.10590.1804-0.0138-0.03680.17340.0030.210650.19893.77558.188
52.41590.0318-0.35051.48490.21972.93920.0617-0.16160.33940.16280.0156-0.0974-0.27570.2523-0.07730.21490.0034-0.02080.114-0.05210.170738.79295.9959.326
60.9423-0.491.13970.8154-0.6682.55990.0745-0.0042-0.09540.0045-0.0147-0.10230.15010.0797-0.05980.1890.0147-0.03890.05250.00750.083336.01671.41681.983
73.22430.23851.3852.1481-0.16136.82680.12370.136-0.1615-0.3835-0.25490.18080.9798-0.16860.13110.45440.00590.01040.191-0.02130.1895-24.37227.30538.104
81.28990.5371-0.33420.94620.36190.4762-0.04120.18790.2553-0.01240.04620.1181-0.0614-0.0505-0.0050.3347-0.0237-0.04380.04780.06130.1405-1.57637.47545.27
91.30050.1142-0.08722.1241-0.24811.83470.0529-0.06070.13770.21530.00080.1957-0.12040.0307-0.05380.2972-0.0128-0.02940.00470.00680.15388.37446.94450.053
103.7627-1.30562.24177.8555-0.08946.5360.0074-0.24040.05330.2123-0.10020.563-0.1342-0.56710.09290.246-0.0144-0.03940.08970.02460.1901-0.21759.55340.071
113.34880.71320.65993.21630.0053.4067-0.05920.28970.0798-0.20050.08410.17120.0658-0.1201-0.02490.23370.0034-0.0380.05260.03450.12756.63446.4634.269
122.89371.11070.46290.87280.39851.21420.0026-0.02720.2483-0.0261-0.02870.1719-0.066-0.16480.02620.28980.008-0.0330.03890.0420.1985-11.336.77841.269
131.2229-0.38380.64432.1197-0.251.7806-0.05570.03040.0813-0.09090.02290.2547-0.1123-0.16010.03280.19180.0087-0.05640.06460.00360.109527.10988.19216.36
140.50150.25730.08970.2352-0.24931.26020.0175-0.05250.0234-0.0336-0.00350.06570.0137-0.0293-0.01390.20180.0209-0.04880.03930.01330.095525.63681.48648.247
152.65010.70412.9092.88-0.998515.1457-0.13150.0541-0.26930.02790.1618-0.07870.1865-0.0505-0.03040.17060.0413-0.00920.0636-0.01890.124632.23869.58746.543
163.0866-0.0360.08882.282-0.1211.58970.03520.152-0.2717-0.132-0.0167-0.02520.2012-0.0087-0.01840.21330.0005-0.04980.0402-0.01610.095416.72568.26743.958
170.58370.2639-0.28240.4169-0.30891.6357-0.0506-0.0340.0589-0.020.0430.07590.0365-0.06140.00770.18910.0114-0.04410.01540.00630.079724.68581.94434.038
1810.78921.9232-6.19517.14111.23134.3825-0.18460.178-0.3180.4757-0.08760.02840.3086-0.15450.27230.331-0.008-0.01550.166-0.01340.210537.90272.9686.269
193.5679-0.56281.96134.76721.6444.3613-0.16610.7599-0.251-0.23440.868-0.484-0.09821.6395-0.70190.3766-0.05280.06180.6879-0.30020.255739.43449.50860.085
201.1485-2.306-1.61644.79834.02088.01250.62690.443-0.5408-1.1623-0.56820.91910.22892.3939-0.05870.6790.7872-0.32182.0375-0.59760.798548.41943.91669.763
213.98151.3363.90481.66131.88565.92360.14230.1803-0.46440.31420.3023-0.3780.44130.5889-0.44460.32950.0667-0.10420.1869-0.0470.212431.94747.78771.888
220.81220.369-0.07721.44370.6461.54390.1374-0.24620.1330.4807-0.11690.2019-0.01730.0571-0.02050.414-0.05270.02980.0927-0.01770.14453.07237.82364.222
231.60991.6424-0.53581.8351-0.19261.54190.1206-0.1799-0.08950.3243-0.1316-0.11560.17840.15650.01090.42370.005-0.08260.07930.02420.138115.00533.2363.473
246.87354.07934.12857.62763.2263.2105-0.3790.2760.2325-0.11570.3525-0.0839-0.43970.4070.02640.2665-0.0039-0.03930.145-0.03060.139733.48359.5672.648
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 75
2X-RAY DIFFRACTION2A76 - 166
3X-RAY DIFFRACTION3A167 - 201
4X-RAY DIFFRACTION4A202 - 222
5X-RAY DIFFRACTION5A223 - 277
6X-RAY DIFFRACTION6A278 - 321
7X-RAY DIFFRACTION7B3 - 75
8X-RAY DIFFRACTION8B76 - 127
9X-RAY DIFFRACTION9B128 - 165
10X-RAY DIFFRACTION10B166 - 194
11X-RAY DIFFRACTION11B195 - 252
12X-RAY DIFFRACTION12B253 - 317
13X-RAY DIFFRACTION13C3 - 80
14X-RAY DIFFRACTION14C81 - 150
15X-RAY DIFFRACTION15C151 - 167
16X-RAY DIFFRACTION16C168 - 243
17X-RAY DIFFRACTION17C244 - 315
18X-RAY DIFFRACTION18C316 - 322
19X-RAY DIFFRACTION19D3 - 32
20X-RAY DIFFRACTION20D33 - 45
21X-RAY DIFFRACTION21D46 - 100
22X-RAY DIFFRACTION22D101 - 230
23X-RAY DIFFRACTION23D231 - 295
24X-RAY DIFFRACTION24D296 - 319

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