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- PDB-2dvm: NAD complex structure of PH1275 protein from Pyrococcus horikoshii -

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Basic information

Entry
Database: PDB / ID: 2dvm
TitleNAD complex structure of PH1275 protein from Pyrococcus horikoshii
Components439aa long hypothetical malate oxidoreductase
KeywordsOXIDOREDUCTASE / malic enzyme / NAD / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


malic enzyme activity / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / metal ion binding
Similarity search - Function
Malic enzyme, NAD-binding domain, bacterial type / Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain ...Malic enzyme, NAD-binding domain, bacterial type / Malic enzyme, N-terminal domain / Malic enzyme, conserved site / Malic enzymes signature. / Malic oxidoreductase / Malic enzyme, N-terminal domain / Malic enzyme, N-terminal domain / Malic enzyme, NAD-binding / Malic enzyme, N-terminal domain superfamily / Malic enzyme, N-terminal domain / Malic enzyme, NAD binding domain / Malic enzyme, NAD binding domain / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 439aa long hypothetical malate oxidoreductase (NAD) [malic enzyme]
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLokanath, N.K. / Mizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: NAD complex structure of PH1275 protein from Pyrococcus horikoshii
Authors: Lokanath, N.K. / Mizutani, H. / Kunishima, N.
History
DepositionJul 31, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 439aa long hypothetical malate oxidoreductase
B: 439aa long hypothetical malate oxidoreductase
C: 439aa long hypothetical malate oxidoreductase
D: 439aa long hypothetical malate oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,49411
Polymers192,2544
Non-polymers3,2397
Water32,9671830
1
A: 439aa long hypothetical malate oxidoreductase
B: 439aa long hypothetical malate oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8446
Polymers96,1272
Non-polymers1,7174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12600 Å2
ΔGint-82 kcal/mol
Surface area30780 Å2
MethodPISA, PQS
2
C: 439aa long hypothetical malate oxidoreductase
D: 439aa long hypothetical malate oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6495
Polymers96,1272
Non-polymers1,5223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-84 kcal/mol
Surface area30890 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.856, 74.294, 141.157
Angle α, β, γ (deg.)90.00, 100.37, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
439aa long hypothetical malate oxidoreductase / malic enzyme


Mass: 48063.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): 21-CodonPlus (DE3)-RIL
References: UniProt: O59029, malate dehydrogenase (oxaloacetate-decarboxylating)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1830 / 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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.4
Details: PEG 4000, MES, pH 6.4, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Sep 13, 2005 / Details: RH coated Cylindrical mirror
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 273244 / Num. obs: 272545 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 12.4
Reflection shellResolution: 1.6→1.66 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WW8

1ww8


Resolution: 1.6→29.84 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 1880317.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 13523 5 %RANDOM
Rwork0.191 ---
obs0.191 272545 99.8 %-
all-273244 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3297 Å2 / ksol: 0.345016 e/Å3
Displacement parametersBiso mean: 26.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å21.47 Å2
2---0.92 Å20 Å2
3---0.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.6→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13457 0 212 1830 15499
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.96
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 2252 5 %
Rwork0.247 43117 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3lig.paramlig.top

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