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- PDB-4e77: 2.0A Crystal Structure of a Glutamate-1-Semialdehyde Aminotransfe... -

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Basic information

Entry
Database: PDB / ID: 4.0E+77
Title2.0A Crystal Structure of a Glutamate-1-Semialdehyde Aminotransferase from Yersinia pestis CO92
ComponentsGlutamate-1-semialdehyde 2,1-aminomutase
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / porphyrin biosynthesis
Function / homology
Function and homology information


glutamate-1-semialdehyde 2,1-aminomutase / glutamate-1-semialdehyde 2,1-aminomutase activity / porphyrin-containing compound biosynthetic process / 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
NITRATE ION / Glutamate-1-semialdehyde 2,1-aminomutase / Glutamate-1-semialdehyde 2,1-aminomutase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsBrunzelle, J.S. / Wawrzak, W. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.0A Crystal Structure of a Glutamate-1-Semialdehyde Aminotransferase from Yersinia pestis CO92
Authors: Brunzelle, J.S. / Wawrzak, W. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)46,9883
Polymers46,9031
Non-polymers852
Water6,179343
1
A: Glutamate-1-semialdehyde 2,1-aminomutase
hetero molecules

A: Glutamate-1-semialdehyde 2,1-aminomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,9766
Polymers93,8062
Non-polymers1704
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area8130 Å2
ΔGint-53 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.540, 60.540, 182.480
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-937-

HOH

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Components

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


Mass: 46902.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: hemL, YPDSF_2968 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: A4TPW6, UniProt: Q8ZBL9*PLUS, glutamate-1-semialdehyde 2,1-aminomutase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 2.06 Å3/Da / Density % sol: 40.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20%PEG 3350,0.2M Ca Nitrate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 25, 2010 / Details: Be Lens
RadiationMonochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.97→36.5 Å / Num. all: 28203 / Num. obs: 28203 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 17.8 % / Biso Wilson estimate: 27.56 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 25
Reflection shellResolution: 1.97→2.03 Å / Redundancy: 18.2 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 4.9 / Num. unique all: 2064 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIXmodel building
BUSTER2.8.0refinement
XDSdata reduction
xia2data reduction
SCALAdata scaling
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.9553 / Cor.coef. Fo:Fc free: 0.9396 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1969 1344 5.01 %RANDOM
Rwork0.1604 ---
all0.1622 26804 --
obs0.1622 26804 --
Displacement parametersBiso mean: 30.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.8434 Å20 Å20 Å2
2---1.8434 Å20 Å2
3---3.6869 Å2
Refine analyzeLuzzati coordinate error obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 5 343 3398
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013152HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.964279HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1422SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes72HARMONIC2
X-RAY DIFFRACTIONt_gen_planes474HARMONIC5
X-RAY DIFFRACTIONt_it3152HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.17
X-RAY DIFFRACTIONt_other_torsion2.64
X-RAY DIFFRACTIONt_chiral_improper_torsion409SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3923SEMIHARMONIC4
LS refinement shellResolution: 2→2.08 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2455 139 4.77 %
Rwork0.1821 2777 -
all0.185 2916 -
obs-2916 -

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