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- PDB-1j5p: Crystal structure of aspartate dehydrogenase (TM1643) from Thermo... -

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Basic information

Entry
Database: PDB / ID: 1j5p
TitleCrystal structure of aspartate dehydrogenase (TM1643) from Thermotoga maritima at 1.9 A resolution
ComponentsASPARTATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / TM1643 / ASPARTATE DEHYDROGENASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
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 / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of aspartate dehydrogenase (TM1643) from Thermotoga maritima at 1.9 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jul 18, 2018Group: Advisory / Data collection / Database references
Category: pdbx_database_related / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Jan 25, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. DIMER PRESENT IN CRYSTAL AND MAY REPRESENT THE BIOLOGICALLY SIGNIFICANT OLIGOMER BY HOMOLOGY WITH 1EBF. THE DIMER CAN BE GENERATED BY APPLYING THE FOLLOWING TRANSFORMATIONS. MATRIX = ( -0.00003 -1.00000 0.00000 ) ( -1.00000 0.00003 0.00000 ) ( 0.00000 0.00000 -1.00000 ) TRANSLATION= (63.20332 63.20157 63.10000 )

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ASPARTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7962
Polymers28,1331
Non-polymers6631
Water1,47782
1
A: ASPARTATE DEHYDROGENASE
hetero molecules

A: ASPARTATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5924
Polymers56,2652
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area6540 Å2
ΔGint-25 kcal/mol
Surface area20370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.2, 63.2, 126.2
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ASPARTATE DEHYDROGENASE /


Mass: 28132.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1643 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1X6, L-aspartate oxidase
#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.: 82 / 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: 2.29 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 293 K / Details: 20% PEG 8000, 0.05M KH2PO4, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.93218, 0.979181, 0.978932
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2002
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.932181
20.9791811
30.9789321
ReflectionResolution: 1.8→44.717 Å / Num. obs: 23895 / % possible obs: 98.5 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.93 Å2 / Rsym value: 0.058 / Net I/σ(I): 15.6
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 4 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.758 / % possible all: 88.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
CCP4data reduction
SOLVEphasing
RESOLVEmodel building
CNS1.1refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→44.69 Å / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: STANDARD CNS DICTIONARY, ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2087 10 %RANDOM
Rwork0.224 ---
obs0.224 20858 99.8 %-
all-20858 --
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 0.356781 Å2 / ksol: 36.7745 e/Å3
Displacement parametersBiso mean: 34.9 Å2
Baniso -1Baniso -2Baniso -3
1--3.316 Å20 Å20 Å2
2---3.316 Å20 Å2
3---6.632 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 44 82 1964
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.1121.5
X-RAY DIFFRACTIONc_mcangle_it4.1032
X-RAY DIFFRACTIONc_scbond_it4.3922
X-RAY DIFFRACTIONc_scangle_it6.2312.5
LS refinement shellResolution: 1.9→1.92 Å / Total num. of bins used: 41
RfactorNum. reflection% reflection
Rfree0.3696 39 8.19 %
Rwork0.3002 438 -
obs--88.2 %

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