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- PDB-5bqf: Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 i... -

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Basic information

Entry
Database: PDB / ID: 5bqf
TitleProbable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L(+)-tartaric acid
ComponentsNADP-dependent 2-hydroxyacid dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / DI(HYDROXYETHYL)ETHER / L(+)-TARTARIC ACID / Probable hydroxyacid dehydrogenase protein
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsLangner, K.M. / Shabalin, I.G. / Handing, K.B. / Gasiorowska, O.A. / Stead, M. / Hillerich, B.S. / Chowdhury, S. / Hammonds, J. / Zimmerman, M.D. / Al Obaidi, N. ...Langner, K.M. / Shabalin, I.G. / Handing, K.B. / Gasiorowska, O.A. / Stead, M. / Hillerich, B.S. / Chowdhury, S. / Hammonds, J. / Zimmerman, M.D. / Al Obaidi, N. / 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)U54-GM094662 United States
CitationJournal: to be published
Title: Probable 2-hydroxyacid dehydrogenase from Rhizobium etli CFN 42 in complex with NADP, HEPES and L-tartaric acid
Authors: Langner, K.M. / Shabalin, I.G. / Handing, K.B. / Gasiorowska, O.A. / Chowdhury, S. / Zimmerman, M.D. / Minor, W.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.4Sep 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: NADP-dependent 2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0917
Polymers35,7951
Non-polymers1,2966
Water8,485471
1
A: NADP-dependent 2-hydroxyacid dehydrogenase
hetero molecules

A: NADP-dependent 2-hydroxyacid dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,18214
Polymers71,5902
Non-polymers2,59312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area10340 Å2
ΔGint-46 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.692, 65.692, 151.406
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein NADP-dependent 2-hydroxyacid dehydrogenase


Mass: 35794.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (strain CFN 42 / ATCC 51251) (bacteria)
Strain: CFN 42 / ATCC 51251 / Gene: RHE_CH00179 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) Ril / References: UniProt: Q2KDT2

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Non-polymers , 7 types, 477 molecules

#2: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: 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
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP 10 mM NADP were mixed with 0.2 ul of the MCSG Suite 2 condition #71 (0.2M Na ...Details: 0.2 ul of 15 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide, 0.5 mM TCEP 10 mM NADP were mixed with 0.2 ul of the MCSG Suite 2 condition #71 (0.2M Na tartrate, 20%w/v PEG 3350) and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci). Before crystallization the protein was incubated with 1/50 v/v of 2 mg/ml TEV solution
Temp details: room temperature

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 8, 2014
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 58208 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 15.6 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.035 / Rrim(I) all: 0.072 / Rsym value: 0.063 / Χ2: 1.084 / Net I/av σ(I): 20.531 / Net I/σ(I): 10.9 / Num. measured all: 231378
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
1.45-1.483.90.5471.929050.7590.3130.6330.59299.5
1.48-1.540.46529160.8250.2640.5370.62899.5
1.5-1.5340.37929280.8640.2160.4370.62399.4
1.53-1.5640.31829000.90.180.3670.63299.3
1.56-1.640.27429130.9250.1550.3160.66899.3
1.6-1.6340.23429140.9480.1330.270.65499.2
1.63-1.6740.229180.9580.1130.2310.67399.1
1.67-1.7240.17829050.9690.1010.2060.73398.8
1.72-1.7740.14729050.9780.0830.1690.78498.7
1.77-1.8340.12729260.9810.0720.1460.84698.6
1.83-1.8940.10429160.9880.0580.1191.00998.4
1.89-1.9740.08428970.9920.0470.0971.21198.2
1.97-2.0640.07729220.9930.0430.0881.4797.9
2.06-2.1740.06929090.9930.0380.0791.63797.7
2.17-2.340.06629030.9940.0370.0761.69297.2
2.3-2.4840.06429120.9940.0360.0741.63296.9
2.48-2.733.90.05729280.9950.0320.0661.66796.5
2.73-3.123.80.04928850.9960.0270.0561.59294.7
3.12-3.943.80.04328750.9970.0230.0491.43593.1
3.94-503.90.03929310.9980.0210.0441.54288.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-3000phasing
Cootmodel building
MOLREPphasing
HKL-3000data scaling
HKL-3000data reduction
HKL-3000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4xcv

4xcv


Resolution: 1.45→50 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.1627 / WRfactor Rwork: 0.1363 / FOM work R set: 0.8957 / SU B: 1.98 / SU ML: 0.038 / SU R Cruickshank DPI: 0.0565 / SU Rfree: 0.0589 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / 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
Rfree0.1654 2857 4.9 %RANDOM
Rwork0.1385 ---
obs0.1398 55340 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 144.17 Å2 / Biso mean: 19.704 Å2 / Biso min: 6.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: final / Resolution: 1.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 79 487 3042
Biso mean--14.96 30.88 -
Num. residues----317
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192761
X-RAY DIFFRACTIONr_bond_other_d0.0020.022689
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9953771
X-RAY DIFFRACTIONr_angle_other_deg0.94336201
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5395345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.18723.03132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.44615481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6581530
X-RAY DIFFRACTIONr_chiral_restr0.0830.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213069
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
X-RAY DIFFRACTIONr_mcbond_it1.7590.9821297
X-RAY DIFFRACTIONr_mcbond_other1.7590.9821296
X-RAY DIFFRACTIONr_mcangle_it2.2211.4691627
X-RAY DIFFRACTIONr_rigid_bond_restr2.954379
X-RAY DIFFRACTIONr_sphericity_bonded9.285579
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 225 -
Rwork0.229 4073 -
all-4298 -
obs--99.19 %
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)
12.1408-0.701-0.27621.43870.32840.88180.0572-0.0344-0.09390.0099-0.02280.0785-0.0176-0.1002-0.03450.0627-0.01850.02320.0345-0.00440.020216.702-2.73322.26
20.4636-0.6131-0.53221.38480.610.65760.06520.0816-0.00380.0216-0.06030.0489-0.0639-0.11-0.0050.05560.00960.00490.06360.00180.025623.771-6.1586.689
30.2084-0.2554-0.07891.0632-0.15220.31850.00380.05610.0237-0.0371-0.0154-0.0310.0184-0.06660.01170.0293-0.008-0.0020.04220.00280.018537.71-24.13-7.49
41.4988-0.70810.82274.1053-1.3671.5670.04220.17410.167-0.1203-0.1681-0.2336-0.01160.06460.12590.02990.02180.02190.07710.03910.034436.876-10.228-16.254
50.5685-0.0282-0.12370.5690.03130.8111-0.01020.1003-0.0202-0.0585-0.03540.06730.0153-0.15020.04570.0226-0.0084-0.00710.076-0.01730.011123.107-21.582-8.911
60.90340.1239-0.60841.002-0.67281.9220.1441-0.00610.04750.0991-0.1026-0.0229-0.15530.0868-0.04140.0652-0.00660.01380.0224-0.00370.013929.6811.83510.981
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 43
2X-RAY DIFFRACTION2A44 - 118
3X-RAY DIFFRACTION3A119 - 172
4X-RAY DIFFRACTION4A173 - 195
5X-RAY DIFFRACTION5A196 - 288
6X-RAY DIFFRACTION6A289 - 319

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