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- PDB-1vjo: Crystal structure of Alanine--glyoxylate aminotransferase (ALR100... -

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Basic information

Entry
Database: PDB / ID: 1vjo
TitleCrystal structure of Alanine--glyoxylate aminotransferase (ALR1004) from Nostoc sp. at 1.70 A resolution
Componentsalanine--glyoxylate aminotransferase
KeywordsTRANSFERASE / 17130350 / ALR1004 / ALANINE--GLYOXYLATE AMINOTRANSFERASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


transaminase activity
Similarity search - Function
Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Alanine--glyoxylate aminotransferase
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of an alanine-glyoxylate aminotransferase from Anabaena sp. at 1.70 A resolution reveals a noncovalently linked PLP cofactor
Authors: Han, G.W. / Schwarzenbacher, R. / Page, R. / Jaroszewski, L. / Abdubek, P. / Ambing, E. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / ...Authors: Han, G.W. / Schwarzenbacher, R. / Page, R. / Jaroszewski, L. / Abdubek, P. / Ambing, E. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Haugen, J. / Hornsby, M. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Nigoghossian, E. / Ouyang, J. / Paulsen, J. / Quijano, K. / Reyes, R. / Sims, E. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / von Delft, F. / Wang, X. / West, B. / White, A. / Wolf, G. / Xu, Q. / Zagnitko, O. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionMar 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: alanine--glyoxylate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9972
Polymers43,7501
Non-polymers2471
Water7,620423
1
A: alanine--glyoxylate aminotransferase
hetero molecules

A: alanine--glyoxylate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9944
Polymers87,4992
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area8720 Å2
ΔGint-50 kcal/mol
Surface area25320 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.258, 101.057, 97.252
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-439-

HOH

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Components

#1: Protein alanine--glyoxylate aminotransferase


Mass: 43749.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8YY48, alanine-glyoxylate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / 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: 2.06 Å3/Da / Density % sol: 39.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.06M HEPES, 0.04M HEPES_Na, 12% PEG MME 5000, 0.2M NP_Calcium Chloride , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal grow
*PLUS
pH: 7.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 %PEG5000 MME1reservoir
20.2 M1reservoirpH7.5CaCl2
30.1 MHEPES1reservoir
410 %ethylene glycol1reservoir
510 mMTris1droppH7.8
6150 mM1dropNaCl
722 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 29, 2003 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bent cylindrical Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→31.18 Å / Num. obs: 42759 / % possible obs: 99.2 % / Redundancy: 5.4 % / Biso Wilson estimate: 26.42 Å2 / Rsym value: 0.093 / Net I/σ(I): 11.8
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2 / Num. unique all: 3161 / Rsym value: 0.722 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 39819 / % possible obs: 92 % / Num. measured all: 313619 / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 74.9 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALA4.2)data scaling
SHELXDphasing
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→31.18 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.743 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. UNLIKE FOR PLP IN MANY PDB STRUCTURES, THE DENSITY SHOWS CLEARLY THAT IT IS NOT COVALENTLY BOUND IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.20182 2043 5.1 %RANDOM
Rwork0.15135 ---
obs0.15383 37725 91.97 %-
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: 23.148 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→31.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 16 423 3343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222998
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.964082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7265375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.77623.359128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27815496
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6021525
X-RAY DIFFRACTIONr_chiral_restr0.1130.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022258
X-RAY DIFFRACTIONr_nbd_refined0.2010.21440
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2319
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.245
X-RAY DIFFRACTIONr_mcbond_it1.0771.51926
X-RAY DIFFRACTIONr_mcangle_it1.29423016
X-RAY DIFFRACTIONr_scbond_it2.60631235
X-RAY DIFFRACTIONr_scangle_it3.764.51066
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 162 6.11 %
Rwork0.223 2491 -
Refinement TLS params.Method: refined / Origin x: 25.0623 Å / Origin y: 46.4533 Å / Origin z: 25.2188 Å
111213212223313233
T-0.1132 Å2-0.0252 Å20.0064 Å2--0.1132 Å2-0.0166 Å2---0.117 Å2
L0.936 °20.0145 °2-0.527 °2-0.5168 °20.2503 °2--0.9419 °2
S-0.0922 Å °0.0606 Å °-0.047 Å °0.0538 Å °-0.0051 Å °0.0557 Å °0.1598 Å °-0.1787 Å °0.0972 Å °
Refinement TLS groupSelection: ALL
Refinement
*PLUS
Rfactor Rfree: 0.202 / Rfactor Rwork: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.59

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