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- PDB-3qm2: 2.25 Angstrom Crystal Structure of Phosphoserine Aminotransferase... -

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Basic information

Entry
Database: PDB / ID: 3qm2
Title2.25 Angstrom Crystal Structure of Phosphoserine Aminotransferase (SerC) from Salmonella enterica subsp. enterica serovar Typhimurium
ComponentsPhosphoserine aminotransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phosphoserine transaminase / O-phospho-L-serine:2-oxoglutarate aminotransferase activity / pyridoxine biosynthetic process / L-serine biosynthetic process / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Phosphoserine aminotransferase / 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 ...Phosphoserine aminotransferase / 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
Phosphoserine aminotransferase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsMinasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.25 Angstrom Crystal Structure of Phosphoserine Aminotransferase (SerC) from Salmonella enterica subsp. enterica serovar Typhimurium.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F.
History
DepositionFeb 3, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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.ptnr1_label_seq_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_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

Downloads & links

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Assembly

Deposited unit
A: Phosphoserine aminotransferase
B: Phosphoserine aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3164
Polymers85,2362
Non-polymers802
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-29 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.260, 82.171, 71.925
Angle α, β, γ (deg.)90.00, 95.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoserine aminotransferase / Phosphohydroxythreonine aminotransferase / PSAT


Mass: 42618.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: serC, STM0977 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P55900, phosphoserine transaminase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.5mGr/mL, 0.5M Sodium chloride, 0.01M TRIS-HCL pH 8.3, Screen: PACT (G1), 0.2M Sodium fluoride, 0.1M Bis Tris propane pH 7.5, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 21, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 35281 / Num. obs: 35281 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 14.5
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1758 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BJN

1bjn


Resolution: 2.25→29.95 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 14.312 / SU ML: 0.16
Isotropic thermal model: Atomic Temperature Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.285 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24235 1760 5 %RANDOM
Rwork0.18548 ---
all0.18833 33491 --
obs0.18833 33491 99.58 %-
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: 52.62 Å2
Baniso -1Baniso -2Baniso -3
1--1.3 Å2-0 Å2-2.89 Å2
2--3.64 Å20 Å2
3----2.92 Å2
Refinement stepCycle: LAST / Resolution: 2.25→29.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5114 0 2 208 5324
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225276
X-RAY DIFFRACTIONr_bond_other_d0.0010.023525
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9537158
X-RAY DIFFRACTIONr_angle_other_deg0.87838601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3045663
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.14724.575247
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.82215862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1511528
X-RAY DIFFRACTIONr_chiral_restr0.090.2786
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215963
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021069
X-RAY DIFFRACTIONr_mcbond_it0.9781.53305
X-RAY DIFFRACTIONr_mcbond_other0.241.51350
X-RAY DIFFRACTIONr_mcangle_it1.7925290
X-RAY DIFFRACTIONr_scbond_it2.71531971
X-RAY DIFFRACTIONr_scangle_it4.3044.51868
LS refinement shellResolution: 2.251→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 128 -
Rwork0.267 2367 -
obs-2367 95.41 %
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)
15.5905-1.37620.72582.3949-0.23163.3321-0.1195-0.93210.4190.29460.00060.4696-0.3509-0.67740.11880.3377-0.10070.01030.4343-0.06080.30122.4714.771823.5768
22.70850.66990.37431.55490.45061.9722-0.0160.28890.0348-0.05290.01220.051-0.02550.03840.00390.05790.00630.00890.036-0.00570.043913.38865.80530.3421
32.10140.21260.47451.49860.40612.11060.0692-0.1497-0.12250.1051-0.0717-0.00350.1277-0.03050.00250.0767-0.00650.030.01340.01230.044314.3532.273810.4856
42.52883.51231.704913.19736.71979.51880.2289-0.42650.00690.72590.2186-0.3803-0.2659-0.3704-0.44750.22090.01230.02050.36010.00090.17831.78384.523426.5658
54.8148-0.51410.74061.93780.17473.0080.1306-0.22390.3247-0.154-0.0670.257-0.2872-0.2238-0.06370.0895-0.01080.02610.0542-0.04660.1743-13.86817.5634.1279
62.65270.14-0.27242.7588-1.83086.04010.0844-0.3189-0.32350.46970.04980.50860.4843-1.1082-0.13420.3632-0.0337-0.02410.4848-0.10810.38565.763431.12228.072
71.5051-0.02680.08871.15320.32172.5762-0.0142-0.0727-0.03640.07330.019-0.01060.02520.1849-0.00480.0505-0.01690.00130.02680.00960.060631.182229.841322.6263
81.78050.42180.45511.4480.37851.8018-0.029-0.06850.1002-0.0454-0.09590.1084-0.1301-0.16830.12480.05070.0021-00.02660.00040.084921.632533.37719.4167
97.88515.27681.709113.21493.37743.808-0.3395-0.2666-0.2744-0.28940.04110.72220.0327-0.75530.29850.11870.02610.01460.3334-0.06060.21313.019931.341427.9243
104.11560.39611.09431.57240.11575.30710.065-0.4109-0.42430.276-0.13660.04450.4936-0.59520.07160.2013-0.1030.04530.1098-0.00260.105921.288628.379148.3451
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 70
2X-RAY DIFFRACTION2A71 - 138
3X-RAY DIFFRACTION3A139 - 234
4X-RAY DIFFRACTION4A242 - 264
5X-RAY DIFFRACTION5A265 - 362
6X-RAY DIFFRACTION6B3 - 70
7X-RAY DIFFRACTION7B71 - 138
8X-RAY DIFFRACTION8B139 - 234
9X-RAY DIFFRACTION9B242 - 264
10X-RAY DIFFRACTION10B265 - 362

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