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- PDB-1h2h: Crystal structure of TM1643 -

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Basic information

Entry
Database: PDB / ID: 1h2h
TitleCrystal structure of TM1643
ComponentsHYPOTHETICAL PROTEIN TM1643Hypothesis
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / POSSIBLE NAD-DEPENDENT OXIDOREDUCTASE / PSI / PROTEIN STRUCTURE INITIATIVE / NESG / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM
Function / homology
Function and homology information


aspartate dehydrogenase / aspartate dehydrogenase activity / oxidoreductase activity, acting on the CH-NH2 group of donors, NAD or NADP as acceptor / NAD biosynthetic process / NAD binding / NADP binding
Similarity search - Function
Aspartate dehydrogenase / L-aspartate dehydrogenase / L-aspartate dehydrogenase, prokaryotic / L-aspartate dehydrogenase, archaeal / Aspartate dehydrogenase, C-terminal / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain ...Aspartate dehydrogenase / L-aspartate dehydrogenase / L-aspartate dehydrogenase, prokaryotic / L-aspartate dehydrogenase, archaeal / Aspartate dehydrogenase, C-terminal / Aspartate/homoserine dehydrogenase, NAD-binding / Homoserine dehydrogenase, NAD binding domain / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / L-aspartate dehydrogenase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsYang, Z. / Savchenko, A. / Edwards, A. / Arrowsmith, C. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J. Biol. Chem. / Year: 2003
Title: Aspartate dehydrogenase, a novel enzyme identified from structural and functional studies of TM1643.
Authors: Yang, Z. / Savchenko, A. / Yakunin, A. / Zhang, R. / Edwards, A. / Arrowsmith, C. / Tong, L.
History
DepositionAug 8, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jun 13, 2018Group: Data collection / Database references
Category: citation / diffrn ...citation / diffrn / diffrn_radiation / diffrn_source
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _diffrn.ambient_temp / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_source.pdbx_wavelength_list
Revision 1.4Aug 21, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_database_related / struct_conn
Item: _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYPOTHETICAL PROTEIN TM1643
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5222
Polymers26,8591
Non-polymers6631
Water72140
1
A: HYPOTHETICAL PROTEIN TM1643
hetero molecules

A: HYPOTHETICAL PROTEIN TM1643
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,0444
Polymers53,7172
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+3/21
Buried area6550 Å2
ΔGint-27.9 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.196, 63.196, 125.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HYPOTHETICAL PROTEIN TM1643 / Hypothesis


Mass: 26858.529 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9X1X6
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENTRY IS FROM A STRUCTURAL GENOMICS EXPERIMENT, POSSIBLY AN NAD-DEPENDENT OXIDOREDUCTASE

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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: 48.9 %
Crystal growpH: 6
Details: 0.2M KDIH.PHOSPHATE, 22%PEG1500, 2% ETHYLENE GLYCOL, pH 6.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMHEPES1drop
2500 mM1dropNaCl
320 mg/mlprotein1drop
40.2 M1reservoirKH2PO4
522 %PEG15001reservoir
61 mMEDTA1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 / Wavelength: 0.979 Å
DetectorDate: Jul 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 9409 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 15 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 25
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 15 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 20 / % possible all: 93.2
Reflection
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 10 Å / Num. measured all: 87706 / Rmerge(I) obs: 0.067

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.6→9.99 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 4752669.87 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 613 7.5 %RANDOM
Rwork0.226 ---
obs0.226 8163 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.4843 Å2 / ksol: 0.412419 e/Å3
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-5.34 Å20 Å20 Å2
2--5.34 Å20 Å2
3----10.69 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.6→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1818 0 44 40 1902
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.511.5
X-RAY DIFFRACTIONc_mcangle_it2.62
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 2.6→2.62 Å / Rfactor Rfree error: 0.09 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.325 13 7.3 %
Rwork0.263 165 -
obs--99.4 %
Refinement
*PLUS
Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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