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- PDB-1zh8: Crystal structure of Oxidoreductase (TM0312) from Thermotoga mari... -

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Basic information

Entry
Database: PDB / ID: 1zh8
TitleCrystal structure of Oxidoreductase (TM0312) from Thermotoga maritima at 2.50 A resolution
Componentsoxidoreductase
KeywordsOXIDOREDUCTASE / TM0312 / oxidoreductase (EC 1.1.1.-) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


NADPH regeneration / oxidoreductase activity / nucleotide binding / cytoplasm
Similarity search - Function
Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / 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 ...Gfo/Idh/MocA-like oxidoreductase, C-terminal / Oxidoreductase family, C-terminal alpha/beta domain / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Oxidoreductase (TM0312) from Thermotoga maritima at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: oxidoreductase
B: oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,59511
Polymers76,7522
Non-polymers1,8439
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6320 Å2
ΔGint-25 kcal/mol
Surface area25030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.849, 63.088, 101.172
Angle α, β, γ (deg.)90.00, 104.88, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 5 - 328 / Label seq-ID: 17 - 340

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein oxidoreductase /


Mass: 38375.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM0312 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WYE8, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.68 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 8.0% Ethylene-Glycol, 10.0% PEG-8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2005
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
ReflectionResolution: 2.5→28.96 Å / Num. obs: 27566 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value% possible all
2.5-2.563.80.374220210.374100
2.56-2.643.70.3142.419670.314100
2.64-2.713.70.2732.819240.273100
2.71-2.83.80.233.318520.23100
2.8-2.893.70.1933.918260.193100
2.89-2.993.70.1654.517520.165100
2.99-3.13.80.1475.116920.147100
3.1-3.233.80.1166.116370.116100
3.23-3.373.70.099715520.099100
3.37-3.543.70.0818.214880.081100
3.54-3.733.70.0719.214350.071100
3.73-3.953.70.0689.713520.068100
3.95-4.233.70.0659.412680.065100
4.23-4.563.70.0599.811850.059100
4.56-53.70.069.210940.06100
5-5.593.70.057109840.057100
5.59-6.453.60.05710.58890.057100
6.45-7.913.50.05311.47480.053100
7.91-11.183.40.04511.95810.04599.8
11.18-28.963.20.04712.73190.04794.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.6data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→28 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.246 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.516 / ESU R Free: 0.272
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1382 5 %RANDOM
Rwork0.194 ---
all0.196 ---
obs0.19618 26222 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.297 Å2
Baniso -1Baniso -2Baniso -3
1-1.73 Å20 Å21.08 Å2
2---0.14 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5026 0 118 146 5290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0225303
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.987197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0795649
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91924.844225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.03215897
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7591520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023922
X-RAY DIFFRACTIONr_nbd_refined0.2070.22300
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2238
X-RAY DIFFRACTIONr_metal_ion_refined0.210.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2770.24
X-RAY DIFFRACTIONr_mcbond_it1.29633232
X-RAY DIFFRACTIONr_mcangle_it2.37655219
X-RAY DIFFRACTIONr_scbond_it4.75982150
X-RAY DIFFRACTIONr_scangle_it6.619111978
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2465 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.210.5
MEDIUM THERMAL0.722
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 90 -
Rwork0.238 1832 -
obs--96.78 %
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)
11.0658-0.4597-0.32372.24491.36372.80360.07060.0944-0.0276-0.0967-0.1640.0552-0.0449-0.20340.0934-0.24170.0081-0.0043-0.1510.0173-0.099250.58419.9793-0.4208
21.2314-0.0644-0.77632.52681.87353.81360.1033-0.12280.14270.4454-0.33680.3170.118-0.39340.23350.0416-0.10380.0452-0.0082-0.0833-0.057639.091935.625942.1249
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 32816 - 340
22BB5 - 32817 - 340

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