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- PDB-5j23: Crystal structure of NADPH-dependent glyoxylate/hydroxypyruvate r... -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5j23
TitleCrystal structure of NADPH-dependent glyoxylate/hydroxypyruvate reductase SMc04462 (SmGhrB) from Sinorhizobium meliloti in complex with 2'-phospho-ADP-ribose
Components2-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / 2-hydroxyacid dehydrogenase / NADP / NYSGRC / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


hydroxypyruvate reductase [NAD(P)H] activity / glyoxylate reductase (NADPH) activity / NAD binding / metal ion binding / cytosol
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
Chem-A2R / ACETATE ION / 2-hydroxyacid dehydrogenase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsShabalin, I.G. / Gasiorowska, O.A. / Handing, K.B. / Bonanno, J. / Kutner, J. / 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) 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 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Derived calculations / Category: pdbx_related_exp_data_set / pdbx_struct_oper_list
Item: _pdbx_related_exp_data_set.data_reference / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
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
Revision 1.4May 23, 2018Group: Data collection / Experimental preparation / Structure summary
Category: exptl_crystal_grow / struct / Item: _exptl_crystal_grow.pdbx_details / _struct.title
Revision 1.5Aug 15, 2018Group: Data collection / Database references / Category: pdbx_related_exp_data_set / Item: _pdbx_related_exp_data_set.data_reference
Revision 1.6Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Apr 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 1.8Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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: 2-hydroxyacid dehydrogenase
B: 2-hydroxyacid dehydrogenase
C: 2-hydroxyacid dehydrogenase
D: 2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,41618
Polymers137,4344
Non-polymers2,98214
Water10,863603
1
A: 2-hydroxyacid dehydrogenase
C: 2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,2209
Polymers68,7172
Non-polymers1,5037
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7680 Å2
ΔGint-63 kcal/mol
Surface area24230 Å2
MethodPISA
2
B: 2-hydroxyacid dehydrogenase
D: 2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1969
Polymers68,7172
Non-polymers1,4797
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7720 Å2
ΔGint-75 kcal/mol
Surface area24340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.822, 175.822, 136.839
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 3 - 320 / Label seq-ID: 4 - 321

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
2-hydroxyacid dehydrogenase


Mass: 34358.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: SMc04462 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q92LZ4
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-A2R / [(2R,3R,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3-HYDROXY-4-(PHOSPHONOOXY)TETRAHYDROFURAN-2-YL]METHYL [(2R,3S,4R,5R)-3,4,5-TRIHYDROXYTETRAHYDROFURAN-2-YL]METHYL DIHYDROGEN DIPHOSPHATE


Mass: 639.296 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H24N5O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 3.01 Å3/Da / Density % sol: 59.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 ul of 13 mg/ml protein in 10 mM NADPH, 10 mM Glycolic Acid, 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 Suite 2 ...Details: 0.2 ul of 13 mg/ml protein in 10 mM NADPH, 10 mM Glycolic Acid, 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 Suite 2 condition #20 (1.1 M Malonic acid, 0.072 M Succinic acid, 0.15M Ammonium dihydrogen citrate, 0.18 M DL-Malic Acid, 0.096 M Ammonium tartrate, 0.24 M Sodium acetate anhydrous, 0.3 M Sodium formate, pH=7.0) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization, the protein 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.237
11K, H, -L20.763
ReflectionResolution: 2.3→50 Å / Num. obs: 70083 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 45.8 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/av σ(I): 18.22 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.343.90.6621.81100
2.34-2.383.90.6041100
2.38-2.433.90.5181100
2.43-2.483.90.4341100
2.48-2.533.90.381100
2.53-2.593.90.3621100
2.59-2.663.90.3051100
2.66-2.733.90.2531100
2.73-2.813.90.21100
2.81-2.93.90.1611100
2.9-33.90.1381100
3-3.123.90.1111100
3.12-3.263.90.091100
3.26-3.443.90.0761100
3.44-3.653.90.0641100
3.65-3.933.90.055199.9
3.93-4.333.90.0511100
4.33-4.953.90.0431100
4.95-6.243.90.0421100
6.24-503.80.03199.7

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
MOLREPphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z0P

4z0p


Resolution: 2.3→36.67 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 6.243 / SU ML: 0.087 / SU R Cruickshank DPI: 0.0458 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.033
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.169 3434 4.9 %RANDOM
Rwork0.1464 ---
obs0.1475 66631 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.08 Å2 / Biso mean: 46.78 Å2 / Biso min: 25.13 Å2
Baniso -1Baniso -2Baniso -3
1--8.99 Å2-0 Å2-0 Å2
2---8.99 Å2-0 Å2
3---17.99 Å2
Refinement stepCycle: final / Resolution: 2.3→36.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9454 0 179 603 10236
Biso mean--52.04 46.2 -
Num. residues----1272
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0199807
X-RAY DIFFRACTIONr_bond_other_d0.0070.029675
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.98513430
X-RAY DIFFRACTIONr_angle_other_deg1.21322102
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.43751268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.24122.256359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.775151493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5541599
X-RAY DIFFRACTIONr_chiral_restr0.0830.21644
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02111179
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022116
X-RAY DIFFRACTIONr_mcbond_it1.2932.6845087
X-RAY DIFFRACTIONr_mcbond_other1.2812.6825083
X-RAY DIFFRACTIONr_mcangle_it2.024.026348
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A393820.02
12B393820.02
21A391860.04
22C391860.04
31A391300.05
32D391300.05
41B390920.04
42C390920.04
51B388660.05
52D388660.05
61C392320.04
62D392320.04
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 256 -
Rwork0.22 4910 -
all-5166 -
obs--99.02 %
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)
11.4573-0.0286-0.36433.79661.59334.01850.05490.01220.27360.08330.07390.3944-0.2932-0.4217-0.12880.15190.0681-0.00360.21190.16110.2406-19.5170.22987.151
21.00760.1453-0.27944.95421.4746.13670.1677-0.28660.34270.3076-0.02930.2413-0.3871-0.2238-0.13830.23790.05640.02810.28060.04260.3276-17.16970.23497.402
32.0761.6464-0.91651.9375-0.89650.610.1015-0.1570.04090.06060.01950.0602-0.02470.0451-0.1210.13570.02990.02630.09640.03280.0887.88778.38286.11
42.82911.0134-0.0072.49750.13213.62840.2258-0.8004-0.46940.5913-0.2123-0.13650.34750.252-0.01360.2724-0.0099-0.04610.33690.15280.211117.81971.69395.92
53.58811.6510.84172.49490.11371.91010.2296-0.6710.40080.4525-0.2260.1475-0.21570.0077-0.00360.1699-0.02240.08980.2474-0.0210.12889.15885.45392.174
61.52790.5285-1.04642.8108-1.02323.8728-0.11030.019-0.14380.00970.12910.06740.2481-0.2052-0.01890.1024-0.012-0.01810.11670.09210.1753-9.90557.95290.7
72.6456-0.2992-0.24191.95960.59652.3490.0527-0.21190.0866-0.01050.1409-0.296-0.09710.6141-0.19360.1256-0.04820.11870.2556-0.10870.175168.60981.311109.77
80.1225-0.29130.04673.13160.99520.70730.0441-0.04970.02010.10580.1089-0.06290.06980.0513-0.15310.0627-0.01560.0320.1504-0.06030.138164.54151.306103.453
94.39021.17181.061910.25882.38015.63510.0389-0.31950.16560.3402-0.10620.8041-0.1725-0.39950.06720.1069-0.00990.05920.1997-0.01720.17250.43351.431104.655
107.9633-0.4346-2.74015.8540.27543.8134-0.113-0.57620.49960.91950.16140.6012-0.2038-0.3224-0.04830.29590.02510.06380.3194-0.05640.184250.64849.079116.713
113.8516-0.52420.92832.8662-0.22683.653-0.2132-0.79730.22110.9340.1584-0.2043-0.0888-0.09880.05470.3520.0378-0.03910.2926-0.10030.141965.35446.752118.078
121.0265-1.5818-0.68854.5761.54251.041-0.0284-0.20170.07820.28670.1888-0.2990.03950.1064-0.16050.0771-0.04960.01990.1235-0.06220.134862.82768.11108.518
134.5276-0.553-0.60435.1604-0.30025.23010.02620.07550.5755-0.01990.0261-0.2207-0.5540.1482-0.05230.1663-0.01340.05730.1229-0.0740.220443.521101.4968.581
143.3120.9933-0.79470.4868-0.24340.58170.01280.16630.1494-0.11690.1108-0.00510.0032-0.0259-0.12360.13810.02510.03770.0942-0.00510.113323.44986.33468.377
152.96540.8203-0.67822.87420.85975.71850.06310.4062-0.5513-0.46340.0887-0.47290.48990.3117-0.15190.32130.06190.11230.2014-0.07510.266621.06768.31163.677
164.45970.10770.79123.26860.47154.0372-0.06130.79670.0233-0.72010.0276-0.1701-0.06820.19550.03360.30720.00370.09120.27380.0420.123715.40380.8957.29
174.14191.00970.07740.75790.10660.5896-0.00620.27810.2623-0.24990.11230.1285-0.051-0.0417-0.10620.19750.00650.04320.11070.02650.13720.95388.77967.642
181.9142-1.15070.20022.47661.58786.4163-0.0046-0.0284-0.1537-0.01720.1041-0.2950.00170.3026-0.09940.1110.01150.05490.1465-0.00270.208350.47685.00162.473
193.3391-0.7849-0.45484.39320.61444.3316-0.088-0.1756-0.10160.06330.1206-0.30690.23480.3891-0.03270.15490.0311-0.09440.1522-0.00470.137666.89613.45487.317
200.42430.7980.27543.18781.16120.6213-0.01060.0678-0.0421-0.2510.1505-0.07010.03260.0858-0.13990.1225-0.0061-0.06830.1073-0.02650.090860.91828.3483.28
216.35482.81151.12389.4379-4.60583.3944-0.23980.15820.31090.1666-0.4727-0.9951-0.17280.37980.71260.1715-0.03-0.06480.2558-0.13970.519178.96657.85102.47
221.35990.89711.26333.03630.28742.33560.13270.11860.0461-0.45490.06090.59170.0747-0.3532-0.19360.1990.0381-0.08310.3142-0.01510.232350.8349.92584.502
231.51880.01120.22123.1021-0.78652.24150.04370.41770.0868-0.67290.0123-0.21840.01110.1409-0.0560.20560.00690.03350.2166-0.06990.119565.60146.68480.365
242.16140.79081.42552.99042.27863.79690.1039-0.0886-0.20390.086-0.07390.15520.3445-0.2018-0.02990.1293-0.0029-0.06890.0844-0.0170.090351.71617.45285.059
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 41
2X-RAY DIFFRACTION2A42 - 61
3X-RAY DIFFRACTION3A62 - 151
4X-RAY DIFFRACTION4A152 - 219
5X-RAY DIFFRACTION5A220 - 286
6X-RAY DIFFRACTION6A287 - 320
7X-RAY DIFFRACTION7B3 - 75
8X-RAY DIFFRACTION8B76 - 149
9X-RAY DIFFRACTION9B150 - 167
10X-RAY DIFFRACTION10B168 - 203
11X-RAY DIFFRACTION11B204 - 252
12X-RAY DIFFRACTION12B253 - 320
13X-RAY DIFFRACTION13C3 - 43
14X-RAY DIFFRACTION14C44 - 151
15X-RAY DIFFRACTION15C152 - 197
16X-RAY DIFFRACTION16C198 - 243
17X-RAY DIFFRACTION17C244 - 298
18X-RAY DIFFRACTION18C299 - 320
19X-RAY DIFFRACTION19D3 - 41
20X-RAY DIFFRACTION20D42 - 119
21X-RAY DIFFRACTION21D120 - 133
22X-RAY DIFFRACTION22D134 - 191
23X-RAY DIFFRACTION23D192 - 285
24X-RAY DIFFRACTION24D286 - 320

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