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- PDB-4gud: Crystal Structure of Amidotransferase HisH from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 4gud
TitleCrystal Structure of Amidotransferase HisH from Vibrio cholerae
ComponentsImidazole glycerol phosphate synthase subunit HisH
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / alpha-beta sandwich / cytosol
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / histidine biosynthetic process / glutaminase activity / glutamine metabolic process / lyase activity / cytoplasm
Similarity search - Function
Imidazole glycerol phosphate synthase, subunit H / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Imidazole glycerol phosphate synthase subunit HisH
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.911 Å
AuthorsMaltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Amidotransferase HisH from Vibrio cholerae.
Authors: Maltseva, N. / Kim, Y. / Shatsman, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Refinement description / Category: citation / software / Item: _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Imidazole glycerol phosphate synthase subunit HisH
B: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5756
Polymers47,0762
Non-polymers4994
Water4,846269
1
A: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7363
Polymers23,5381
Non-polymers1982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Imidazole glycerol phosphate synthase subunit HisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8393
Polymers23,5381
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.422, 118.234, 42.975
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailstwo monomers in the asymmetric unit

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Imidazole glycerol phosphate synthase subunit HisH / IGP synthase glutamine amidotransferase subunit / IGP synthase subunit HisH / ImGP synthase subunit ...IGP synthase glutamine amidotransferase subunit / IGP synthase subunit HisH / ImGP synthase subunit HisH / IGPS subunit HisH


Mass: 23538.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar El Tor str. N16961 / Gene: hisH, VC_1136 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q9KSX0, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 5 types, 273 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Calcium Chloride, 0.1M TRIS HCl pH 8.5, 25% (w/v) PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2012 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 33885 / Num. obs: 33885 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 19.44 Å2 / Rsym value: 0.125 / Net I/σ(I): 8.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 1669 / Rsym value: 0.37 / % possible all: 99.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXmodel building
ARP/wARPmodel building
PHENIX(phenix.refine: 1.7.3_920)refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.911→32.143 Å / SU ML: 0.17 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.57 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1694 5.04 %random
Rwork0.174 ---
all0.176 33619 --
obs0.176 33619 98.43 %-
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.058 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.8659 Å2-0 Å20 Å2
2---3.8027 Å20 Å2
3---7.6686 Å2
Refinement stepCycle: LAST / Resolution: 1.911→32.143 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3084 0 33 269 3386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053394
X-RAY DIFFRACTIONf_angle_d0.8894614
X-RAY DIFFRACTIONf_dihedral_angle_d14.9241285
X-RAY DIFFRACTIONf_chiral_restr0.061508
X-RAY DIFFRACTIONf_plane_restr0.003613
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.9112-1.96750.24211250.19172448257392
1.9675-2.0310.22791210.172826482789100
2.031-2.10350.21511500.171526572807100
2.1035-2.18770.21491300.176126512781100
2.1877-2.28730.20921440.17662649279399
2.2873-2.40780.25951450.18032665281099
2.4078-2.55860.21271490.17762650279999
2.5586-2.75610.2151440.18192630277499
2.7561-3.03330.22231310.17522700283199
3.0333-3.47170.20791510.17282678282999
3.4717-4.37230.16361520.15382728278099
4.3723-32.14720.20671520.18482821297397
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)
12.67870.3529-0.92543.3466-1.49234.9144-0.01250.1715-0.0729-0.08230.06080.37490.0578-0.2921-0.07210.12160.02380.00370.1415-0.05220.199561.448411.415637.8771
21.4738-0.2255-0.04492.57581.28973.01020.00950.2821-0.0364-0.4324-0.15640.1571-0.0381-0.3840.13110.1454-0.0053-0.00910.1679-0.02320.163267.47074.108526.1846
31.16640.4058-0.70552.3928-0.56821.2652-0.0570.0306-0.0458-0.10950.016-0.18630.07910.00460.03310.0750.0170.00650.0914-0.0020.10470.0883-9.230635.1151
41.57970.6456-0.55652.8899-0.0391.39990.0258-0.0674-0.10420.1056-0.0368-0.1295-0.03830.0027-0.0010.07660.0044-0.03120.09930.00530.0971.1034-4.098438.8714
53.4751-0.61011.78782.88531.13324.61590.18220.3355-0.4285-0.1603-0.00510.13450.3551-0.0912-0.08920.13350.03290.00740.1747-0.05940.226650.632218.999831.0791
62.5948-0.70670.45981.8610.5251.9552-0.0563-0.2006-0.15930.16860.05270.03220.1872-0.13870.02450.1094-0.02030.00160.0862-0.00280.138448.40524.804443.6595
71.92640.50730.00871.14-0.13690.5918-0.01340.03430.2214-0.01480.01310.0541-0.0130.0036-0.01520.0920.0099-0.00180.08710.00340.121233.269828.88636.0131
80.99860.2579-0.38341.1706-0.51530.9949-0.05990.29750.0995-0.2420.0707-0.0395-0.07890.14860.01880.0979-0.04760.0180.17430.03830.014145.604530.861822.7404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:40)
2X-RAY DIFFRACTION2chain 'A' and (resseq 41:99)
3X-RAY DIFFRACTION3chain 'A' and (resseq 100:154)
4X-RAY DIFFRACTION4chain 'A' and (resseq 155:203)
5X-RAY DIFFRACTION5chain 'B' and (resseq 2:25)
6X-RAY DIFFRACTION6chain 'B' and (resseq 26:100)
7X-RAY DIFFRACTION7chain 'B' and (resseq 101:189)
8X-RAY DIFFRACTION8chain 'B' and (resseq 190:209)

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