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Basic information

Entry
Database: PDB / ID: 2x5f
TitleCrystal structure of the methicillin-resistant Staphylococcus aureus Sar2028, an aspartate_tyrosine_phenylalanine pyridoxal-5'-phosphate dependent aminotransferase
ComponentsASPARTATE_TYROSINE_PHENYLALANINE PYRIDOXAL-5' PHOSPHATE-DEPENDENT AMINOTRANSFERASE
KeywordsTRANSFERASE
Function / homology
Function and homology information


Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
Citation
Journal: J.Struct.Funct.Genom. / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Expression, Purification, Crystallization, Data Collection and Preliminary Biochemical Characterization of Methicillin-Resistant Staphylococcus Aureus Sar2028, an ...Title: Expression, Purification, Crystallization, Data Collection and Preliminary Biochemical Characterization of Methicillin-Resistant Staphylococcus Aureus Sar2028, an Aspartate/Tyrosine/Phenylalanine Pyridoxal-5'-Phosphate-Dependent Aminotransferase.
Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G. ...Authors: Seetharamappa, J. / Oke, M. / Liu, H. / Mcmahon, S.A. / Johnson, K.A. / Carter, L. / Dorward, M. / Zawadzki, M. / Overton, I.M. / Van Niekirk, C.A.J. / Graham, S. / Botting, C.H. / Taylor, G.L. / White, M.F. / Barton, G.J. / Coote, P.J. / Naismith, J.H.
History
DepositionFeb 8, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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_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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: ASPARTATE_TYROSINE_PHENYLALANINE PYRIDOXAL-5' PHOSPHATE-DEPENDENT AMINOTRANSFERASE
B: ASPARTATE_TYROSINE_PHENYLALANINE PYRIDOXAL-5' PHOSPHATE-DEPENDENT AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,8789
Polymers96,6932
Non-polymers1,1857
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10660 Å2
ΔGint-57.2 kcal/mol
Surface area30380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.780, 89.990, 104.910
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: LEU / Beg label comp-ID: LEU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 2 / Auth seq-ID: 4 - 33 / Label seq-ID: 6 - 35

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ASPARTATE_TYROSINE_PHENYLALANINE PYRIDOXAL-5' PHOSPHATE-DEPENDENT AMINOTRANSFERASE


Mass: 48346.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: 252 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6GFC0, UniProt: A0A7U7EVR5*PLUS

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Non-polymers , 5 types, 236 molecules

#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE (PLP): THERE IS AN OXYGEN ATOM MISSING FROM PLP

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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: 2.02 Å3/Da / Density % sol: 39.18 % / Description: NONE
Crystal growpH: 7.5
Details: 28% PEG3350, 0.1M HEPES PH 7.5. THE CRYSTALS WERE CRYOPROTECTED WITH 16% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 15, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.8→27.24 Å / Num. obs: 69033 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 3.01 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDEphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.8→27.24 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.395 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.026 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21049 3667 5 %RANDOM
Rwork0.19099 ---
obs0.19198 69033 99.26 %-
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 mean: 7.184 Å2
Baniso -1Baniso -2Baniso -3
1--17.54 Å20 Å20 Å2
2--8.62 Å20 Å2
3---8.92 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6783 0 71 229 7083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227027
X-RAY DIFFRACTIONr_bond_other_d0.0030.024604
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.969555
X-RAY DIFFRACTIONr_angle_other_deg0.927311316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70525.479334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.225151184
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.0831521
X-RAY DIFFRACTIONr_chiral_restr0.0670.21063
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217787
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021346
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4181.54285
X-RAY DIFFRACTIONr_mcbond_other0.1181.51721
X-RAY DIFFRACTIONr_mcangle_it0.74126944
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.52932742
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.414.52607
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A180tight positional0.030.05
2B180tight positional0.030.05
1A210medium positional0.080.5
2B210medium positional0.080.5
1A180tight thermal0.10.5
2B180tight thermal0.10.5
1A210medium thermal0.112
2B210medium thermal0.112
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 269 -
Rwork0.232 4873 -
obs--96.91 %
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)
15.8923-2.5723-2.21393.04972.12793.2827-0.1282-0.81810.12570.38110.3122-0.29920.22980.5588-0.1840.34760.0115-0.03730.1799-0.00740.034225.97544.29912.269
24.0778-0.5463.26350.1166-0.41862.6317-0.213-0.51290.42280.1505-0.0047-0.0958-0.1081-0.39080.21760.576-0.020.07110.2575-0.10230.358549.21552.072-4.395
31.7779-0.0969-0.52650.29670.04820.74640.0602-0.06910.28580.01160.001-0.0051-0.0949-0.0348-0.06110.3202-0.0009-0.00540.0148-0.00550.056115.56655.714-2.903
43.30760.23320.22731.1369-0.05230.83860.01470.53740.1717-0.1588-0.0316-0.0169-0.0398-0.08590.0170.36170.05240.01040.18850.08110.0454-0.89959.131-23.086
52.4026-1.5101-0.23934.68510.34532.97330.06840.0398-0.5533-0.0274-0.12220.49180.1834-0.39950.05380.322-0.0555-0.00560.0634-0.01320.133314.28626.317-13.158
68.5561.4635-0.11040.26640.04710.3868-0.07510.6144-0.3975-0.0380.0469-0.0902-0.056-0.22310.02820.4430.05350.05230.22890.05660.176514.8655.642-27.109
71.41210.0585-0.04830.7936-0.06510.79630.0040.0617-0.19190.0005-0.0034-0.07820.10770.0442-0.00060.29450.00530.00090.0059-0.00850.032635.44532.715-15.476
84.37990.82930.91722.7265-0.55812.28780.1698-0.51740.14910.3957-0.2517-0.1933-0.19990.09010.0820.3375-0.0441-0.00490.13010.00760.094558.71542.412-4.114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 34
2X-RAY DIFFRACTION2A35 - 61
3X-RAY DIFFRACTION3A62 - 321
4X-RAY DIFFRACTION4A322 - 428
5X-RAY DIFFRACTION5B0 - 33
6X-RAY DIFFRACTION6B34 - 74
7X-RAY DIFFRACTION7B75 - 331
8X-RAY DIFFRACTION8B332 - 427

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