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- PDB-4n18: Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 4n18
TitleCrystal structure of D-isomer specific 2-hydroxyacid dehydrogenase family protein from Klebsiella pneumoniae 342
ComponentsD-isomer specific 2-hydroxyacid dehydrogenase family protein
KeywordsOXIDOREDUCTASE / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC / D-isomer specific 2-hydroxyacid dehydrogenase family protein
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / cytosol
Similarity search - Function
D-isomer specific 2-hydroxyacid dehydrogenases signature 3. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site / 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 / D-isomer specific 2-hydroxyacid dehydrogenase family protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsBacal, P. / Shabalin, I.G. / Cooper, D.R. / Majorek, K.A. / Osinski, T. / Hillerich, B.S. / Hammonds, J. / Nawar, A. / Stead, M. / Chowdhury, S. ...Bacal, P. / Shabalin, I.G. / Cooper, D.R. / Majorek, K.A. / Osinski, T. / Hillerich, B.S. / Hammonds, J. / Nawar, A. / Stead, M. / Chowdhury, S. / Gizzi, A. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase family protein from Klebsiella pneumoniae 342
Authors: Bacal, P. / Shabalin, I.G. / Cooper, D.R. / Majorek, K.A. / Osinski, T. / Hillerich, B.S. / Hammonds, J. / Nawar, A. / Stead, M. / Chowdhury, S. / Gizzi, A. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W.
History
DepositionOct 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-isomer specific 2-hydroxyacid dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6273
Polymers37,0801
Non-polymers5472
Water2,036113
1
A: D-isomer specific 2-hydroxyacid dehydrogenase family protein
hetero molecules

A: D-isomer specific 2-hydroxyacid dehydrogenase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,2536
Polymers74,1602
Non-polymers1,0934
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area5960 Å2
ΔGint-23 kcal/mol
Surface area26710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.567, 76.567, 101.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein D-isomer specific 2-hydroxyacid dehydrogenase family protein


Mass: 37080.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Strain: 342 / Gene: KPK_1152 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: B5XVG7
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.2 ul of 15 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 0.2 ul of The MCSG-I condition #88 (0.1M Sodium Citrate:HCL pH 5. ...Details: 0.2 ul of 15 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 0.2 ul of The MCSG-I condition #88 (0.1M Sodium Citrate:HCL pH 5.6, 20% (v/v) 2-Propanol, 20% (w/v)PEG 4000) and equilibrated against 1.9 M NaCl in QIAGEN EasyXtal 15-Well Tool plate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 20, 2013
Details: Rosenbaum-Rock vertical focusing mirror, with Pt, glass, Pd lanes
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: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. all: 22004 / Num. obs: 21916 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Χ2: 1.961 / Net I/σ(I): 44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym valueΧ2% possible all
1.97-29.50.9891.910501.90.77297.8
2-2.0410.30.79610550.80398.7
2.04-2.0811.20.68610710.82499.4
2.08-2.1211.30.54410770.83299.9
2.12-2.1711.20.43110750.855100
2.17-2.2211.30.35610690.912100
2.22-2.2711.20.30310780.928100
2.27-2.3411.30.25110810.984100
2.34-2.411.20.20910881.002100
2.4-2.4811.20.18810971.09100
2.48-2.5711.20.1610711.217100
2.57-2.6711.20.12411101.298100
2.67-2.811.20.110791.493100
2.8-2.9411.10.08311001.708100
2.94-3.13110.07311002.087100
3.13-3.37110.06211212.465100
3.37-3.7110.90.05811063.294100
3.71-4.2410.60.0611354.4799.6
4.24-5.3510.40.05111424.68999.6
5.35-509.60.05812117.56597

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→35.84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.463 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 1124 5.1 %RANDOM
Rwork0.1812 ---
obs0.1833 21871 99.64 %-
all-21950 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 102.44 Å2 / Biso mean: 45.1758 Å2 / Biso min: 27.26 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å2-0 Å20 Å2
2---1.35 Å2-0 Å2
3---2.71 Å2
Refinement stepCycle: LAST / Resolution: 1.97→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2383 0 26 113 2522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192491
X-RAY DIFFRACTIONr_bond_other_d0.0010.022366
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9673392
X-RAY DIFFRACTIONr_angle_other_deg0.86935414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1785312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.48523.246114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27315361
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3371520
X-RAY DIFFRACTIONr_chiral_restr0.1080.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02594
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 67 -
Rwork0.246 1474 -
all-1541 -
obs-1541 97.78 %
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)
125.2128-15.21797.998212.272-6.9044.8629-0.0816-0.7554-1.63260.25660.43850.86610.1958-0.1847-0.35690.2788-0.0346-0.00260.11510.09440.1366-6.49838.27211.759
23.0368-1.3256-1.9792.20311.1773.8363-0.33540.171-0.19620.11760.02240.18820.1241-0.5190.3130.1793-0.0197-0.02320.22610.03690.0929-1.09623.5224.074
33.8044-2.8343-0.5844.09250.91532.01010.03140.387-0.3539-0.2017-0.09050.4331-0.086-0.29890.05910.0845-0.0362-0.0420.16020.01460.06430.37622.45816.475
40.0412-0.14120.10991.0086-1.50763.8752-0.05460.00790.0039-0.0057-0.1076-0.08720.1688-0.04640.16230.14450.01790.0180.2140.01110.019311.81916.79427.53
50.6980.7496-0.82711.579-0.36571.7017-0.3053-0.0938-0.1510.1304-0.0742-0.01250.60960.15470.37950.41160.03140.13920.16720.02310.090512.2680.24156.738
63.3093-1.55920.07992.74331.58035.9801-0.04940.17160.1641-0.1976-0.022-0.1457-0.4450.33990.07140.1847-0.02630.03080.12860.0370.026424.88412.20339.588
71.7225-0.24370.31890.52970.67652.301-0.06510.1672-0.2415-0.0853-0.13610.07640.205-0.08780.20110.2026-0.02190.06770.1146-0.03420.067715.1840.06736.322
82.5339-1.7605-0.76943.4654-0.13884.38330.0246-0.15190.5926-0.15330.2029-0.7808-0.4290.2765-0.22750.1388-0.08640.01190.1884-0.0150.226412.79229.14821.907
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 3
2X-RAY DIFFRACTION2A4 - 25
3X-RAY DIFFRACTION3A26 - 55
4X-RAY DIFFRACTION4A56 - 108
5X-RAY DIFFRACTION5A109 - 137
6X-RAY DIFFRACTION6A138 - 169
7X-RAY DIFFRACTION7A170 - 278
8X-RAY DIFFRACTION8A279 - 308

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