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- PDB-3t32: Crystal structure of a putative C-S lyase from Bacillus anthracis -

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Basic information

Entry
Database: PDB / ID: 3t32
TitleCrystal structure of a putative C-S lyase from Bacillus anthracis
ComponentsAminotransferase, class I/II
KeywordsLYASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / aminotransferase
Function / homology
Function and homology information


transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
Putative C-S lyase / 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 ...Putative C-S lyase / 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
Aminotransferase, class I/II / Aminotransferase, classes I and II
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Gordon, E. / Peterson, S.N. / Porebski, P. / Minor, W. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative C-S lyase from Bacillus anthracis
Authors: Anderson, S.M. / Wawrzak, Z. / Gordon, E. / Peterson, S.N. / Porebski, P. / Minor, W. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 24, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionAug 10, 2011ID: 3KAX
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Sep 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminotransferase, class I/II
B: Aminotransferase, class I/II


Theoretical massNumber of molelcules
Total (without water)89,2072
Polymers89,2072
Non-polymers00
Water8,143452
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-24 kcal/mol
Surface area28460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.291, 84.655, 170.750
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminotransferase, class I/II / Aminotransferase / classes I and II / putative C-S lyase


Mass: 44603.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: BAS4776, BA_5138, GBAA_5138 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81K67, UniProt: A0A6L7H8L3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 452 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG3350, 200mM potassium sulphate, 10mM pyridoxyl-5-phosphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12714 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 11, 2010 / Details: bimorph KB mirrors
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12714 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 52327 / Num. obs: 51856 / % possible obs: 99.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 2.3 / Redundancy: 4.3 % / Biso Wilson estimate: 28.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 15
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 2.3 / Num. unique all: 5164 / % possible all: 97.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KAX

3kax
PDB Unreleased entry


Resolution: 2→28.5 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8586 / SU ML: 0.44 / σ(F): 1.35 / σ(I): 2.35 / Phase error: 20.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2066 2599 5.03 %random
Rwork0.1736 ---
all0.1755 52139 --
obs0.1753 51696 99.2 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.344 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 158.08 Å2 / Biso mean: 38.8 Å2 / Biso min: 12 Å2
Baniso -1Baniso -2Baniso -3
1-4.3708 Å2-0 Å2-0 Å2
2---9.3184 Å20 Å2
3---4.9476 Å2
Refinement stepCycle: LAST / Resolution: 2→28.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5826 0 0 452 6278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076013
X-RAY DIFFRACTIONf_angle_d0.8968185
X-RAY DIFFRACTIONf_chiral_restr0.058903
X-RAY DIFFRACTIONf_plane_restr0.0041050
X-RAY DIFFRACTIONf_dihedral_angle_d13.3472239
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2-2.03640.28851130.249925412654265597.8
2.0364-2.07550.28111270.23525232650265198.6
2.0755-2.11790.23081160.216625632679267999.4
2.1179-2.16390.23671340.192325702704270599.7
2.1639-2.21420.24311170.189725762693269399.7
2.2142-2.26960.21431570.186725702727272899.9
2.2696-2.33090.22371410.193225432684268599.9
2.3309-2.39950.24341400.1896258027202721100
2.3995-2.47690.23421450.178925802725272799.8
2.4769-2.56530.21141250.1887260527302730100
2.5653-2.6680.21641350.182525632698269899.9
2.668-2.78930.23611390.188925962735273599.9
2.7893-2.93620.21571280.19326112739273999.6
2.9362-3.120.21591400.186125832723272499.5
3.12-3.36050.22431340.185525922726272699.3
3.3605-3.69810.19221530.166125962749274999
3.6981-4.23170.18261560.136725932749274998.6
4.2317-5.32580.1771580.136126072765276697.9
5.3258-28.48650.18031410.168727052846285196
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)
11.587-0.9015-1.04653.62280.12111.38640.20730.12840.0039-0.5331-0.1291-0.1384-0.0041-0.0712-0.06170.443-0.0361-0.06520.3322-0.02910.219610.72522.557310.7127
21.77770.04860.37932.13570.10051.82090.0156-0.07550.00740.0648-0.00790.1233-0.0039-0.080.00590.1018-0.01410.01690.12350.02390.14745.672221.051733.957
32.8829-0.3693-1.51571.59710.5083.9298-0.0345-0.1722-0.2810.13260.0180.14710.19450.0144-0.0150.1257-0.0238-0.00110.16890.04710.20494.55710.75942.0761
41.0606-0.2733-0.18282.24370.12640.98680.06450.1519-0.0563-0.29320.00570.17990.0396-0.1202-0.06640.1546-0.0225-0.03350.19840.02050.16041.951721.928525.9872
55.3346-2.80932.26344.6745-1.49532.59610.26440.1217-0.6292-0.5058-0.03680.25770.4875-0.0267-0.24410.3805-0.0556-0.03390.1691-0.06220.282411.5329-0.333417.3969
62.2112-1.00340.79221.99650.74463.083-0.0076-0.101-0.15640.00410.0559-0.17080.23530.3306-0.03210.14870.02140.04740.15630.04270.297825.70863.66230.4316
73.26220.67330.81961.35080.10284.6903-0.08680.4376-0.407-0.44630.1847-0.38750.45260.5834-0.07690.36220.02320.0870.2451-0.05840.342624.94750.403219.8501
80.00810.0877-0.03391.525-0.74042.1835-0.00910.04-0.1032-0.53960.10590.10660.09560.0803-0.02850.6203-0.03680.11440.32950.02430.208410.939736.2997.3409
90.9693-0.03820.16361.2456-0.40560.9699-0.03310.07340.1309-0.1729-0.0743-0.4302-0.11330.1473-0.00860.1693-0.01090.08120.1580.04480.239919.754749.562524.654
101.1872-0.4060.03721.5317-0.26561.2934-0.13470.12760.1977-0.40890.19650.0857-0.0699-0.11720.06840.41350.0353-0.00370.28620.17930.30073.356761.762610.4964
111.2449-0.17070.91070.27310.11094.0467-0.12140.26490.2218-0.49470.27660.4636-0.1305-0.5523-0.14660.4295-0.0565-0.11730.34640.18270.3079-2.848359.54512.0073
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 24:63)
2X-RAY DIFFRACTION2chain 'A' and (resseq 64:138)
3X-RAY DIFFRACTION3chain 'A' and (resseq 139:195)
4X-RAY DIFFRACTION4chain 'A' and (resseq 196:280)
5X-RAY DIFFRACTION5chain 'A' and (resseq 281:305)
6X-RAY DIFFRACTION6chain 'A' and (resseq 306:358)
7X-RAY DIFFRACTION7chain 'A' and (resseq 359:383)
8X-RAY DIFFRACTION8chain 'B' and (resseq 24:63)
9X-RAY DIFFRACTION9chain 'B' and (resseq 64:280)
10X-RAY DIFFRACTION10chain 'B' and (resseq 281:340)
11X-RAY DIFFRACTION11chain 'B' and (resseq 341:383)

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