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- PDB-2ho5: Crystal structure of Oxidoreductase, Gfo/Idh/MocA family from Str... -

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Basic information

Entry
Database: PDB / ID: 2ho5
TitleCrystal structure of Oxidoreductase, Gfo/Idh/MocA family from Streptococcus pneumoniae
ComponentsOxidoreductase, Gfo/Idh/MocA family
KeywordsOXIDOREDUCTASE / Gfo/Idh/MocA family / Streptococcus pneumoniae / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Oxidoreductase, Gfo/Idh/MocA family / Oxidoreductase, Gfo/Idh/MocA family
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.56 Å
AuthorsChang, C. / Hatzos, C. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of Oxidoreductase, Gfo/Idh/MocA family from Streptococcus pneumoniae
Authors: Chang, C. / Hatzos, C. / Abdullah, J. / Joachimiak, A.
History
DepositionJul 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, Gfo/Idh/MocA family
B: Oxidoreductase, Gfo/Idh/MocA family


Theoretical massNumber of molelcules
Total (without water)73,3852
Polymers73,3852
Non-polymers00
Water23413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-10 kcal/mol
Surface area25920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.113, 117.113, 102.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Oxidoreductase, Gfo/Idh/MocA family /


Mass: 36692.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pMCSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative / References: UniProt: Q97PV8, UniProt: A0A0H2UR04*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 13 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris, 25% PEG3350, pH 8.5, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 23819 / Num. obs: 23462 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 31.4 % / Rmerge(I) obs: 0.153 / Net I/σ(I): 67.67
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 13.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 3.07 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.56→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.912 / SU B: 25.929 / SU ML: 0.257 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.734 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26627 1197 5.1 %RANDOM
Rwork0.21085 ---
obs0.21367 22126 98.08 %-
all-22126 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 76.237 Å2
Baniso -1Baniso -2Baniso -3
1-1.68 Å20 Å20 Å2
2--1.68 Å20 Å2
3----3.35 Å2
Refinement stepCycle: LAST / Resolution: 2.56→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4820 0 0 13 4833
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0224954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9296728
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5035610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.95724.754244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26415794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9021514
X-RAY DIFFRACTIONr_chiral_restr0.1250.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.22335
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.23327
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0580.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9211.53102
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40624865
X-RAY DIFFRACTIONr_scbond_it2.31832090
X-RAY DIFFRACTIONr_scangle_it3.3914.51861
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.56→2.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 72 -
Rwork0.327 1358 -
obs--83.87 %
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)
13.0488-0.45691.71314.18250.46626.3666-0.31740.12940.17240.08470.20740.1339-0.6516-0.65040.11-0.23660.20050.0490.1536-0.125-0.2851-3.2138.2795.87
21.9888-0.62051.39942.9151-0.85673.924-0.3862-0.47140.34290.43470.2680.1443-0.3894-0.79440.1182-0.28150.1890.0654-0.0116-0.1476-0.36213.69832.04123.394
32.711-0.69390.55282.891-0.53862.3426-0.0837-0.1463-0.04040.12460.11150.17570.1869-0.5328-0.0278-0.23720.03490.0632-0.0594-0.0588-0.383610.59619.90525.395
45.9489-0.81832.6716.59490.06416.47650.2504-1.3221-0.72481.2095-0.1285-0.04750.9125-0.069-0.12190.43680.1501-0.10370.26540.0136-0.011441.269-1.66644.95
52.6489-1.50291.25313.7730.51923.9356-0.0954-0.1052-0.0930.03240.2599-0.53080.50290.3094-0.1645-0.15180.05780.0498-0.1829-0.053-0.407933.3763.70127.693
63.0149-0.61030.5494.22311.35994.0735-0.0409-0.4082-0.03430.333-0.00120.18380.4913-0.42970.042-0.137-0.01920.0372-0.1239-0.0222-0.403320.8710.1126.64
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1191 - 119
2X-RAY DIFFRACTION2AA120 - 139120 - 139
3X-RAY DIFFRACTION2AA172 - 192172 - 192
4X-RAY DIFFRACTION2AA276 - 320276 - 320
5X-RAY DIFFRACTION3AA140 - 153140 - 153
6X-RAY DIFFRACTION3AA193 - 275193 - 275
7X-RAY DIFFRACTION4BB1 - 1191 - 119
8X-RAY DIFFRACTION5BB120 - 139120 - 139
9X-RAY DIFFRACTION5BB172 - 192172 - 192
10X-RAY DIFFRACTION5BB276 - 320276 - 320
11X-RAY DIFFRACTION6BB140 - 153140 - 153
12X-RAY DIFFRACTION6BB193 - 275193 - 275

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