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- PDB-3k28: Crystal Structure of a glutamate-1-semialdehyde aminotransferase ... -

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Basic information

Entry
Database: PDB / ID: 3k28
TitleCrystal Structure of a glutamate-1-semialdehyde aminotransferase from Bacillus anthracis with bound Pyridoxal 5'Phosphate
ComponentsGlutamate-1-semialdehyde 2,1-aminomutase 2
Keywordsisomerase / transferase / Biosynthesis of cofactors / prosthetic groups / and carriers / CSGID / Cytoplasm / Porphyrin biosynthesis / Pyridoxal phosphate / Structural Genomics / National Institute of Allergy and Infectious Diseases / National Institutes of Health / Department of Health and Human Services / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


glutamate-1-semialdehyde 2,1-aminomutase / glutamate-1-semialdehyde 2,1-aminomutase activity / protoporphyrinogen IX biosynthetic process / transaminase activity / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase / 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 ...Tetrapyrrole biosynthesis, glutamate-1-semialdehyde aminotransferase / 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
PYRIDOXAL-5'-PHOSPHATE / Glutamate-1-semialdehyde 2,1-aminomutase 2
Similarity search - Component
Biological speciesBacillus anthracis str. 'Ames Ancestor' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsSharma, S.S. / Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of a glutamate-1-semialdehyde aminotransferase from Bacillus anthracis with bound Pyridoxal 5'Phosphate
Authors: Sharma, S.S. / Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate-1-semialdehyde 2,1-aminomutase 2
B: Glutamate-1-semialdehyde 2,1-aminomutase 2
C: Glutamate-1-semialdehyde 2,1-aminomutase 2
D: Glutamate-1-semialdehyde 2,1-aminomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,57922
Polymers187,0484
Non-polymers1,53118
Water27,0231500
1
A: Glutamate-1-semialdehyde 2,1-aminomutase 2
B: Glutamate-1-semialdehyde 2,1-aminomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,29011
Polymers93,5242
Non-polymers7669
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10980 Å2
ΔGint-117 kcal/mol
Surface area25520 Å2
MethodPISA
2
C: Glutamate-1-semialdehyde 2,1-aminomutase 2
D: Glutamate-1-semialdehyde 2,1-aminomutase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,29011
Polymers93,5242
Non-polymers7669
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10900 Å2
ΔGint-116 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.809, 113.688, 113.955
Angle α, β, γ (deg.)90.00, 118.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Glutamate-1-semialdehyde 2,1-aminomutase 2 / GSA 2 / Glutamate-1-semialdehyde aminotransferase 2 / GSA-AT 2


Mass: 46762.004 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria)
Strain: Ames Ancestor / Gene: BAS4358, BA_4693, GBAA_4693, hemL-2, hemL2 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic
References: UniProt: Q81LD0, glutamate-1-semialdehyde 2,1-aminomutase
#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 1500 / 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: 2.28 Å3/Da / Density % sol: 45.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 18% PEG8K, 0.2M caAcet., 0.1M Nacacod pH 6.5, 10mM PLP , VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 31, 2009 / Details: Be lens
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 240968 / Num. obs: 240968 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 20.82 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 17.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.58 / Num. unique all: 11981 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
CRANKphasing
ARP/wARPmodel building
BUSTER2.8.0refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→28.45 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1854 6110 5.02 %RANDOM
Rwork0.1473 ---
obs-121762 --
Displacement parametersBiso mean: 23.28 Å2
Baniso -1Baniso -2Baniso -3
1-6.1679 Å20 Å21.0357 Å2
2---0.9231 Å20 Å2
3----5.2449 Å2
Refine analyzeLuzzati coordinate error obs: 0.162 Å
Refinement stepCycle: LAST / Resolution: 1.95→28.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12922 0 74 1513 14509
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2323 429 4.76 %
Rwork0.1779 8590 -
obs-8590 -

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