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- PDB-1say: L-ALANINE DEHYDROGENASE COMPLEXED WITH PYRUVATE -

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Basic information

Entry
Database: PDB / ID: 1say
TitleL-ALANINE DEHYDROGENASE COMPLEXED WITH PYRUVATE
ComponentsL-ALANINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / NAD
Function / homology
Function and homology information


alanine dehydrogenase / alanine dehydrogenase activity / L-alanine catabolic process / nucleotide binding
Similarity search - Function
Alanine dehydrogenase / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, conserved site-2 / Alanine dehydrogenase & pyridine nucleotide transhydrogenase signature 2. / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / 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/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / 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
PYRUVIC ACID / Alanine dehydrogenase
Similarity search - Component
Biological speciesPhormidium lapideum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS WITH NATIVE ENZYME / 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-ALANINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6802
Polymers38,5921
Non-polymers881
Water1,72996
1
A: L-ALANINE DEHYDROGENASE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)232,08212
Polymers231,5546
Non-polymers5286
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 area22140 Å2
ΔGint-31 kcal/mol
Surface area76550 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)122.400, 122.400, 183.000
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-557-

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: Chemical ChemComp-PYR / PYRUVIC ACID / Pyruvic acid


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 3.42 Å3/Da / Density % sol: 63.99 %
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: Jan 21, 1997 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 63279 / % possible obs: 96.2 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.5 / % possible all: 99.1
Reflection shell
*PLUS
% possible obs: 99.1 %

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Processing

Software
NameVersionClassification
CCP4model building
TNT5Erefinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: ISOMORPHOUS WITH NATIVE ENZYME
Resolution: 2.1→30 Å / Isotropic thermal model: TNT / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.25 -5 %RANDOM
Rwork0.18 ---
all-28636 --
obs-28636 78 %-
Solvent computationSolvent model: MOEWS AND KRETSINGER
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2715 0 6 96 2817
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01527681.5
X-RAY DIFFRACTIONt_angle_deg1.1637503
X-RAY DIFFRACTIONt_dihedral_angle_d18.116580
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.009694
X-RAY DIFFRACTIONt_gen_planes0.0154049
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg18.10
X-RAY DIFFRACTIONt_plane_restr0.0159

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