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- PDB-3hmu: Crystal structure of a class III aminotransferase from Silicibact... -

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Basic information

Entry
Database: PDB / ID: 3hmu
TitleCrystal structure of a class III aminotransferase from Silicibacter pomeroyi
ComponentsAminotransferase, class III
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / Aminotransferase / Pyridoxal phosphate / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


transaminase activity / pyridoxal phosphate binding
Similarity search - Function
Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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 ...Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / 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
Aminotransferase, class III
Similarity search - Component
Biological speciesSilicibacter pomeroyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsToro, R. / Bonanno, J.B. / Ramagopal, U. / Freeman, J. / Bain, K.T. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a class III aminotransferase from Silicibacter pomeroyi
Authors: Toro, R. / Bonanno, J.B. / Ramagopal, U. / Freeman, J. / Bain, K.T. / Miller, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Nov 28, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.5Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase, class III
B: Aminotransferase, class III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,8946
Polymers103,6312
Non-polymers2634
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11490 Å2
ΔGint-119 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.246, 113.605, 130.985
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminotransferase, class III


Mass: 51815.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter pomeroyi (bacteria) / Gene: SPO3471 / Plasmid: modified pET26 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5LMU1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 100mM sodium cacodylate pH 6.5, 30% PEG 8K, 200mM ammonium sulfate, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97958 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2009
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 56821 / Num. obs: 56398 / % possible obs: 99.26 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 13.9 Å2 / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Χ2: 1.17 / Net I/σ(I): 9.884
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.74 / Num. unique all: 2738 / Rsym value: 0.31 / Χ2: 0.941 / % possible all: 94.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.17 / WRfactor Rwork: 0.133 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.897 / SU B: 3.701 / SU ML: 0.099 / SU R Cruickshank DPI: 0.19 / SU Rfree: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2840 5.1 %RANDOM
Rwork0.15 ---
obs0.152 56166 99.13 %-
all-56659 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 50.98 Å2 / Biso mean: 13.518 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7104 0 12 666 7782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217271
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9459868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3085922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38824.154337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.504151183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6631548
X-RAY DIFFRACTIONr_chiral_restr0.1020.21075
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215600
X-RAY DIFFRACTIONr_mcbond_it0.6971.54577
X-RAY DIFFRACTIONr_mcangle_it1.30127321
X-RAY DIFFRACTIONr_scbond_it2.67132694
X-RAY DIFFRACTIONr_scangle_it4.2164.52547
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 199 -
Rwork0.17 3777 -
all-3976 -
obs-3777 96.93 %

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