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- PDB-1pjb: L-ALANINE DEHYDROGENASE -

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Basic information

Entry
Database: PDB / ID: 1pjb
TitleL-ALANINE DEHYDROGENASE
ComponentsL-ALANINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD
Function / homology
Function and homology information


alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / nucleotide binding / plasma membrane
Similarity search - Function
Alanine dehydrogenase / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding Rossmann-like Domain ...Alanine dehydrogenase / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alanine dehydrogenase
Similarity search - Component
Biological speciesPhormidium lapideum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsBaker, P.J. / Sawa, Y. / Shibata, H. / Sedelnikova, S.E. / Rice, D.W.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Analysis of the structure and substrate binding of Phormidium lapideum alanine dehydrogenase.
Authors: Baker, P.J. / Sawa, Y. / Shibata, H. / Sedelnikova, S.E. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Crystallization of the Alanine Dehydrogenase from Phormidium Lapideum
Authors: Sedelnikova, S. / Rice, D.W. / Shibata, H. / Sawa, Y. / Baker, P.J.
#2: Journal: J.Biochem.(Tokyo) / Year: 1994
Title: Purification and Characterization of Alanine Dehydrogenase from a Cyanobacterium, Phormidium Lapideum
Authors: Sawa, Y. / Tani, M. / Murata, K. / Shibata, H. / Ochiai, H.
History
DepositionJun 5, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-ALANINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)38,5921
Polymers38,5921
Non-polymers00
Water1,78399
1
A: L-ALANINE DEHYDROGENASE
x 6


Theoretical massNumber of molelcules
Total (without water)231,5546
Polymers231,5546
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area20350 Å2
ΔGint-78 kcal/mol
Surface area77490 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.100, 123.100, 184.860
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-401-

HOH

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Components

#1: Protein L-ALANINE DEHYDROGENASE


Mass: 38592.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phormidium lapideum (bacteria) / Description: MATSUE HOT SPRINGS / Gene: ALADH / Plasmid: PNAD1 / Gene (production host): ALADH / Production host: Escherichia coli (E. coli) / Strain (production host): MV1184 / References: UniProt: O52942, alanine dehydrogenase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 3.49 Å3/Da / Density % sol: 64.76 %
Crystal growpH: 6.7 / Details: pH 6.7
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125-30 mg/mlprotein1drop
20.1 MMES1drop
36-10 %PEG200001reservoir
40.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 29, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→18 Å / Num. obs: 82395 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.033 / Net I/σ(I): 14.5
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 2.9 / % possible all: 91.2
Reflection shell
*PLUS
% possible obs: 91.2 %

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Processing

Software
NameVersionClassification
CCP4model building
TNTrefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→30 Å / Isotropic thermal model: TNT / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Rfactor% reflectionSelection details
Rfree0.25 5 %RANDOM
Rwork0.19 --
obs-86 %-
Solvent computationSolvent model: MOEWS AND KRETSINGER
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 0 99 2814
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.019
X-RAY DIFFRACTIONt_angle_deg1.4
X-RAY DIFFRACTIONt_dihedral_angle_d18.3
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.3

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