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- PDB-3od1: The crystal structure of an ATP phosphoribosyltransferase regulat... -

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Basic information

Entry
Database: PDB / ID: 3od1
TitleThe crystal structure of an ATP phosphoribosyltransferase regulatory subunit/histidyl-tRNA synthetase from Bacillus halodurans C
ComponentsATP phosphoribosyltransferase regulatory subunit
KeywordsTRANSFERASE / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


histidyl-tRNA aminoacylation / histidine-tRNA ligase activity / L-histidine biosynthetic process / transferase activity / cytoplasm
Similarity search - Function
Rossmann fold - #12590 / : / Histidyl-tRNA synthetase HisZ, C-terminal domain / ATP phosphoribosyltransferase regulatory subunit / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II ...Rossmann fold - #12590 / : / Histidyl-tRNA synthetase HisZ, C-terminal domain / ATP phosphoribosyltransferase regulatory subunit / Histidine-tRNA ligase/ATP phosphoribosyltransferase regulatory subunit / Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain / Histidyl-tRNA synthetase / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / ATP phosphoribosyltransferase regulatory subunit
Similarity search - Component
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.97 Å
AuthorsTan, K. / Bigelow, L. / Hamilton, J. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of aATP phosphoribosyltransferase regulatory subunit/histidyl-tRNA synthetase from Bacillus halodurans C
Authors: Tan, K. / Bigelow, L. / Hamilton, J. / Bearden, J. / Joachimiak, A.
History
DepositionAug 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ATP phosphoribosyltransferase regulatory subunit
B: ATP phosphoribosyltransferase regulatory subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7237
Polymers90,2772
Non-polymers4475
Water6,179343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint-26 kcal/mol
Surface area30980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.696, 63.255, 107.637
Angle α, β, γ (deg.)90.00, 105.72, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. It is predicted that the chains A and B form a dimer.

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Components

#1: Protein ATP phosphoribosyltransferase regulatory subunit


Mass: 45138.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C / Gene: BH3584, hisZ / Plasmid: pMCSG19b / Production host: Escherichia coli (E. coli) / Strain (production host): pPK1037 / References: UniProt: Q9K6Z0
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 12% PEG4000, 0.1M Sodium Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97967 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 22, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97967 Å / Relative weight: 1
ReflectionResolution: 1.97→26 Å / Num. all: 65055 / Num. obs: 65055 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 25.3
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 2 / Num. unique all: 3270 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.97→25.677 Å / SU ML: 0.27 / σ(F): 0 / σ(I): 0 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 3092 5.06 %random
Rwork0.1792 ---
all0.1815 61166 --
obs0.1815 61166 91.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.984 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.8857 Å20 Å2-5.0471 Å2
2--1.741 Å2-0 Å2
3---2.1447 Å2
Refinement stepCycle: LAST / Resolution: 1.97→25.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5980 0 26 343 6349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076135
X-RAY DIFFRACTIONf_angle_d1.028269
X-RAY DIFFRACTIONf_dihedral_angle_d17.6982272
X-RAY DIFFRACTIONf_chiral_restr0.068924
X-RAY DIFFRACTIONf_plane_restr0.0041064
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9703-2.04070.30212200.23934615X-RAY DIFFRACTION73
2.0407-2.12230.2532830.20435580X-RAY DIFFRACTION89
2.1223-2.21890.26012960.19225472X-RAY DIFFRACTION87
2.2189-2.33580.23853010.20935875X-RAY DIFFRACTION92
2.3358-2.4820.24583320.1785965X-RAY DIFFRACTION95
2.482-2.67350.23523470.18296140X-RAY DIFFRACTION97
2.6735-2.94220.23213660.17746167X-RAY DIFFRACTION98
2.9422-3.36710.23833190.18566292X-RAY DIFFRACTION99
3.3671-4.23910.20113230.15696135X-RAY DIFFRACTION96
4.2391-25.67870.19383050.16145833X-RAY DIFFRACTION90
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)
10.7003-0.28590.35920.3666-0.32620.68760.01610.04210.04140.0338-0.0164-0.00350.0707-0.0143-0.00010.2642-0.00010.01390.21750.0010.206486.587615.073832.6422
20.4443-0.20110.25890.23140.02060.49530.1965-0.76050.11810.1340.2539-0.09120.06770.2099-0.40460.23540.01110.09880.472-0.07640.514645.932842.097928.4296
30.46510.20980.25350.8237-0.10360.9522-0.02670.04320.0938-0.1060.06120.20660.0505-0.0809-0.0320.2045-0.0286-0.03390.27510.05710.289855.404528.87457.5116
41.86190.27420.410.83-0.47130.97020.35670.15890.9637-0.0921-0.16580.1463-0.03970.2594-0.10430.2702-0.04130.06090.32050.02470.549296.863939.012230.5817
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A resid 2:325
2X-RAY DIFFRACTION2chain A resid 330:388
3X-RAY DIFFRACTION3chain B resid 1:327
4X-RAY DIFFRACTION4chain B resid 331:388

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