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- PDB-4rkc: Psychrophilic aromatic amino acids aminotransferase from Psychrob... -

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Basic information

Entry
Database: PDB / ID: 4rkc
TitlePsychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6
ComponentsAromatic amino acid aminotransferase
KeywordsTRANSFERASE / AMINOTRANSFERASE / AROMATIC SUBSTRATES / PLP Dependent ENZYME / PLP
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / identical protein binding / metal ion binding / cytosol
Similarity search - Function
Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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 ...Aspartate/other aminotransferase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / 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
NITRATE ION / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Aminotransferase
Similarity search - Component
Biological speciesPsychrobacter sp. B6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsBujacz, A. / Rutkiewicz-Krotewicz, M. / Bujacz, G. / Nowakowska-Sapota, K. / Turkiewicz, M.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6.
Authors: Bujacz, A. / Rutkiewicz-Krotewicz, M. / Nowakowska-Sapota, K. / Turkiewicz, M.
History
DepositionOct 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / diffrn_source / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model / 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 / _entity.formula_weight / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_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: Aromatic amino acid aminotransferase
B: Aromatic amino acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,56316
Polymers88,3982
Non-polymers1,16514
Water13,890771
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-33 kcal/mol
Surface area28120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.687, 62.106, 85.895
Angle α, β, γ (deg.)90.00, 102.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aromatic amino acid aminotransferase


Mass: 44199.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Psychrobacter sp. B6 (bacteria) / Strain: B6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: C7E5X4, aromatic-amino-acid transaminase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13N2O5P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 771 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M Mg(NO3)2, 20% PEG3350, 0.1M Hepes pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.802 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 9, 2011 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. obs: 39647 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 16.67
Reflection shellResolution: 2.19→2.27 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 3.72 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FSL and 3QN6

3fsl

3qn6


Resolution: 2.19→43 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.554 / SU ML: 0.119 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20316 1989 5 %RANDOM
Rwork0.14207 ---
all0.14517 ---
obs0.14517 37644 99.62 %-
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: 25.137 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20 Å2-0.52 Å2
2--0.57 Å2-0 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.19→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6202 0 74 771 7047
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0196462
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.9748746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635808
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5524.459296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.348151072
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1821536
X-RAY DIFFRACTIONr_chiral_restr0.1350.2947
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214976
X-RAY DIFFRACTIONr_mcbond_it1.9781.9823199
X-RAY DIFFRACTIONr_mcangle_it2.962.9644000
X-RAY DIFFRACTIONr_scbond_it2.8332.1973263
X-RAY DIFFRACTIONr_long_range_B_refined6.78317.93811846
LS refinement shellResolution: 2.19→2.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 159 -
Rwork0.184 2636 -
obs--95.98 %
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)
10.11850.00620.13280.1411-0.0030.1908-0.06460.05280.01180.01750.00430.0105-0.07810.05370.06030.0532-0.0203-0.00340.03360.00140.050132.945237.686256.6462
20.32070.1132-0.02220.23030.10990.41810.0116-0.0321-0.01560.0136-0.009-0.0099-0.00090.0304-0.00260.00990.00380.00710.00840.00590.010836.488623.645175.3729
30.58950.47890.3141.04190.27741.0549-0.03460.02050.03940.0155-0.022-0.0531-0.22520.08610.05660.0544-0.0208-0.01620.01120.01120.016748.804341.724664.0242
40.34530.02710.12250.108-0.03730.09290.02880.0814-0.06240.0191-0.00390.00130.00520.0425-0.0250.01310.012-0.00270.0276-0.01390.01219.878114.024953.7894
50.54330.091-0.06150.14550.08090.20550.00980.00760.0073-0.0109-0.04890.0179-0.0546-0.06170.03910.02630.0232-0.00620.0329-0.00780.01385.540431.55660.8556
60.49080.2826-0.02620.7616-0.14130.2089-0.01390.054-0.0275-0.01770.01660.08610.017-0.0018-0.00260.0130.0158-0.00390.0328-0.01250.02222.769211.206847.2993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 66
2X-RAY DIFFRACTION2A67 - 287
3X-RAY DIFFRACTION3A288 - 398
4X-RAY DIFFRACTION4B1 - 66
5X-RAY DIFFRACTION5B67 - 287
6X-RAY DIFFRACTION6B288 - 398

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