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- PDB-1omo: alanine dehydrogenase dimer w/bound NAD (archaeal) -

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Basic information

Entry
Database: PDB / ID: 1omo
Titlealanine dehydrogenase dimer w/bound NAD (archaeal)
Componentsalanine dehydrogenase
KeywordsOXIDOREDUCTASE / two-domain / beta-sandwich-dimer / Rossmann-fold NAD domain / human mu crystallin homolog / human thyroid-hormone-binder homolog
Function / homology
Function and homology information


alanine metabolic process / alanine dehydrogenase / alanine dehydrogenase activity / NAD binding / protein homodimerization activity
Similarity search - Function
Alanine dehydrogenase, Archaeoglobus-type / Alanine dehydrogenase, archaeal-type / ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Alanine dehydrogenase, Archaeoglobus-type / Alanine dehydrogenase, archaeal-type / ornithine cyclodeaminase, domain 1 / ornithine cyclodeaminase, domain 1 / Ornithine cyclodeaminase/mu-crystallin / Ornithine cyclodeaminase, N-terminal / Ornithine cyclodeaminase/mu-crystallin family / 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 / Alanine dehydrogenase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.32 Å
AuthorsGallagher, D.T. / Smith, N.N. / Holden, M.J. / Schroeder, I. / Monbouquette, H.G.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Structure of alanine dehydrogenase from Archaeoglobus: active site analysis and relation to bacterial cyclodeaminases and mammalian mu crystallin.
Authors: Gallagher, D.T. / Monbouquette, H.G. / Schroeder, I. / Robinson, H. / Holden, M.J. / Smith, N.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and phasing of alanine dehydrogenase from Archaeoglobus fulgidus.
Authors: Smith, N. / Mayhew, M. / Robinson, H. / Heroux, A. / Charlton, D. / Holden, M.J. / Gallagher, D.T.
History
DepositionFeb 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE SEQUENCE MATCHES GENBANK ENTRY NP_070493 AND TIGR SEQUENCE AF1665. HOWEVER, ACCORDING ...SEQUENCE THE SEQUENCE MATCHES GENBANK ENTRY NP_070493 AND TIGR SEQUENCE AF1665. HOWEVER, ACCORDING TO THE AUTHOR, THE PROTEIN NAME ASSIGNED FOR THE GENBANK ENTRY IS INCORRECT. THE PROTEIN WAS ASSIGNED THE NAME ORNITHINE CYCLODEAMINASE BASED ON SEQUENCE HOMOLOGY, BUT THE AUTHORS STATE THE PROTEIN HAS BEEN SHOWN TO BE AN ALANINE DEHYDROGENASE. THE GENBANK REFERENCE IS NOT USED FOR THE DBREF SINCE THE PROTEIN NAME IS INCORRECTLY ASSIGNED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alanine dehydrogenase
B: alanine dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,1136
Polymers69,7402
Non-polymers1,3734
Water6,089338
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-62 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.7, 55.5, 131.3
Angle α, β, γ (deg.)90, 111.1, 90
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-714-

HOH

Detailsthe asymmetric unit contains the biological dimer

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Components

#1: Protein alanine dehydrogenase /


Mass: 34869.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / Strain (production host): MZ1 / References: UniProt: O28608, alanine dehydrogenase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 338 / 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: 2.65 Å3/Da / Density % sol: 53.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: Protein 15 mg/mL, MPD (~20%), 100 mM NaCl, 10 mM Tris, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.088,1.1048,1.1051
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2002
RadiationMonochromator: silicon cut crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0881
21.10481
31.10511
ReflectionResolution: 2.3→30 Å / Num. all: 32620 / Num. obs: 32447 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 17.6
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 3.1 % / % possible all: 98

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.32→8 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.262 1189 quasirandom throughout 4%
Rwork0.203 --
all0.213 29537 -
obs0.213 29537 -
Displacement parametersBiso mean: 32.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.28 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.32→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4852 0 90 338 5280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.89
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d1.65
LS refinement shellResolution: 2.32→2.46 Å / Rfactor Rfree error: 0.023
RfactorNum. reflection% reflection
Rfree0.292 185 -
Rwork0.248 --
obs-4563 92.6 %

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