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- PDB-1vll: Crystal structure of alanine dehydrogenase (AF1665) from Archaeog... -

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Basic information

Entry
Database: PDB / ID: 1vll
TitleCrystal structure of alanine dehydrogenase (AF1665) from Archaeoglobus fulgidus at 2.80 A resolution
Componentsalanine dehydrogenase
KeywordsOXIDOREDUCTASE / 2648890 / AF1665 / alanine dehydrogenase / structural genomics / JCSG / protein structure initiative / PSI / Joint Center for Structural Genomics
Function / homology
Function and homology information


alanine metabolic process / alanine dehydrogenase / alanine dehydrogenase activity / NAD binding / protein homodimerization activity / cytoplasm
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
Alanine dehydrogenase
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of alanine dehydrogenase (AF1665) from Archaeoglobus fulgidus at 2.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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


Theoretical massNumber of molelcules
Total (without water)72,6632
Polymers72,6632
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3990 Å2
ΔGint-40 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.702, 92.437, 131.783
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 2 / Auth seq-ID: 1 - 321 / Label seq-ID: 13 - 333

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein alanine dehydrogenase


Mass: 36331.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF1665, arcB / Production host: Escherichia coli (E. coli) / References: UniProt: O28608, alanine dehydrogenase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.3848.22
22.754.03DATA FROM A CRYSTAL CONTAINING SE-MET SUBSTITUTED WAS USED FOR THE MAD PHASING EXPERIMENTS AND DATA FROM A CRYSTAL OF THE NATIVE PROTEIN WAS USED FOR THE FINAL REFINEMENT. THE 3 ANGSTROM MAD PHASES WERE EXTENDED TO 2.8 ANGSTROMS USING THE NATIVE STRUCTURE FACTOR AMPLITUDES IN THE PROGRAM RESOLVE. AFTER THE INITIAL TRACE PDB ENTRY 1OMO WAS USED TO FACILITATE COMPLETION OF THE MODEL.
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, sitting drop, nanodrop0.05M Acetic Acid, 0.052M Citrate_Na3, 29% PEG MME 550 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
2932vapor diffusion, sitting drop, nanodrop0.05M Acetic Acid, 0.05M Citrate_Na3, 30% PEG MME 550 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONALS 8.3.111.11588
SYNCHROTRONALS 8.2.120.9794, 0.9796, 1.0000
Detector
TypeIDDetectorDate
ADSC1CCDFeb 4, 2004
ADSC2CCDSep 20, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double Crystal Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.115881
20.97941
30.97961
411
ReflectionResolution: 2.8→56.7 Å / Num. obs: 17713 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 84.89 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.8
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1280 / % possible all: 99.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→52.09 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 37.347 / SU ML: 0.317 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.378
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: THE DATA USED IN THE FINAL REFINEMENT WAS FROM A NATIVE CRYSTAL. THE REFINEMENT OF THE COORDINATES WAS RESTRAINED WITH THE EXPERIMENTAL PHASES FROM A CRYSTAL OF THE SELENOMETHIONINE- ...Details: THE DATA USED IN THE FINAL REFINEMENT WAS FROM A NATIVE CRYSTAL. THE REFINEMENT OF THE COORDINATES WAS RESTRAINED WITH THE EXPERIMENTAL PHASES FROM A CRYSTAL OF THE SELENOMETHIONINE-SUBSTITUTED PROTEIN THAT WAS USED FOR INITIAL PHASE DETERMINATION BY MULTIPLE WAVELENGTH ANOMALOUS DISPERSION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2539 897 5.1 %RANDOM
Rwork0.21742 ---
obs0.21926 16757 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 49.558 Å2
Baniso -1Baniso -2Baniso -3
1--1.6 Å20 Å20 Å2
2---1.47 Å20 Å2
3---3.08 Å2
Refinement stepCycle: LAST / Resolution: 2.8→52.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4574 0 0 0 4574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224654
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.9616342
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8365640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.52624.737171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34615669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6721518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2747
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023540
X-RAY DIFFRACTIONr_nbd_refined0.2190.22113
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2160
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.23
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.240.21
X-RAY DIFFRACTIONr_mcbond_it1.18433241
X-RAY DIFFRACTIONr_mcangle_it2.04954991
X-RAY DIFFRACTIONr_scbond_it4.20481588
X-RAY DIFFRACTIONr_scangle_it6.284111351
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23218
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1284tight positional0.050.05
952medium positional0.380.5
1284tight thermal0.150.5
952medium thermal1.072
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 71 5.59 %
Rwork0.377 1200 -
obs--99.61 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0116-0.6774-1.10262.3470.94184.0827-0.1603-0.3431-0.23110.54040.1076-0.0233-0.0141-0.16670.05270.00350.056-0.113-0.02870.0342-0.0003-5.752-14.7739-18.4681
22.5881-0.9114-0.96213.49690.91432.95370.03860.23930.17-0.85990.2334-0.46-0.31890.2956-0.2720.0963-0.27540.01590.09640.10640.138322.2799-19.1183-47.0774
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 1 - 321 / Label seq-ID: 13 - 333

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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