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- PDB-4hkm: Crystal Structure of an Anthranilate Phosphoribosyltransferase (t... -

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Basic information

Entry
Database: PDB / ID: 4hkm
TitleCrystal Structure of an Anthranilate Phosphoribosyltransferase (target ID NYSGRC-016600) from Xanthomonas campestris
ComponentsAnthranilate phosphoribosyltransferase
KeywordsTRANSFERASE / Structural Genomics / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


anthranilate phosphoribosyltransferase / anthranilate phosphoribosyltransferase activity / tryptophan biosynthetic process / magnesium ion binding / cytosol
Similarity search - Function
Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain ...Anthranilate phosphoribosyl transferase / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C / Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2 / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Glycosyl transferase family 3, N-terminal domain / Glycosyl transferase family 3, N-terminal domain superfamily / Glycosyl transferase family, helical bundle domain / Glycosyl transferase, family 3 / Glycosyl transferase family, a/b domain / Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Anthranilate phosphoribosyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.953 Å
AuthorsGhosh, A. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of an Anthranilate Phosphoribosyltransferase (target ID NYSGRC-016600) from Xanthomonas campestris
Authors: Ghosh, A. / Ahmed, A. / Banu, R. / Bhoshle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Seidel, R. / ...Authors: Ghosh, A. / Ahmed, A. / Banu, R. / Bhoshle, R. / Bonanno, J. / Chamala, S. / Chowdhury, S. / Fiser, A. / Glenn, A.S. / Hillerich, B. / Khafizov, K. / Lafleur, J. / Love, J.D. / Seidel, R. / Stead, M. / Toro, R. / Almo, S.C.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Data collection / Database references / Refinement description
Category: citation_author / diffrn_radiation / software
Item: _citation_author.name / _diffrn_radiation.pdbx_diffrn_protocol ..._citation_author.name / _diffrn_radiation.pdbx_diffrn_protocol / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Anthranilate phosphoribosyltransferase
B: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,59011
Polymers74,6152
Non-polymers9759
Water4,432246
1
A: Anthranilate phosphoribosyltransferase
hetero molecules

A: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1798
Polymers74,6152
Non-polymers5646
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3000 Å2
ΔGint-33 kcal/mol
Surface area25080 Å2
MethodPISA
2
B: Anthranilate phosphoribosyltransferase
hetero molecules

A: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,59011
Polymers74,6152
Non-polymers9759
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3300 Å2
ΔGint-32 kcal/mol
Surface area25700 Å2
MethodPISA
3
B: Anthranilate phosphoribosyltransferase
hetero molecules

B: Anthranilate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,00114
Polymers74,6152
Non-polymers1,38712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area4300 Å2
ΔGint-50 kcal/mol
Surface area25620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.25, 161.13, 56.3
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsThere are 2 biological units (a dimer) in the asymmetric unit (chains A, B)

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Components

#1: Protein Anthranilate phosphoribosyltransferase


Mass: 37307.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: ATCC 33913 / NCPPB 528 / LMG 568 / Gene: trpD, XCC0469 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pRIL
References: UniProt: Q8PD71, anthranilate phosphoribosyltransferase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 0.2 M Lithium Sulfate, 0.1 M CAPS:NaOH, 1.2 M NaH2PO4/0.8 M K2HPO4, pH 10.5, vapor diffusion, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9790, 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 27, 2012
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.0751
ReflectionResolution: 1.95→50 Å / Num. all: 50053 / Num. obs: 49820 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.7 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.093 / Χ2: 1.284 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-1.987.80.78324891.4251,2100
1.98-2.027.80.61624821.4511,2100
2.02-2.067.80.52224691.4471,2100
2.06-2.17.80.42525001.4641,2100
2.1-2.157.90.37225281.4361,2100
2.15-2.27.90.324621.4411,2100
2.2-2.257.90.26325131.41,2100
2.25-2.317.90.2324881.3761,2100
2.31-2.3880.19424841.3581,2100
2.38-2.4680.1725361.2971,2100
2.46-2.5480.15625121.3141,2100
2.54-2.6580.1424941.2351,2100
2.65-2.7780.12425381.211,2100
2.77-2.9180.10825181.1711,2100
2.91-3.17.90.09425371.1251,2100
3.1-3.337.80.08525341.0831,299.6
3.33-3.677.50.07725031.1851,298.6
3.67-4.26.90.06224611.1451,295
4.2-5.296.60.05324180.9981,293
5.29-507.20.04525871.0371,293.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
HKL-3000data reduction
SOLVEphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.953→43.414 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8191 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 2538 5.09 %RANDOM
Rwork0.1867 ---
obs0.1888 47282 98.58 %-
all-49820 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 132.04 Å2 / Biso mean: 36.6434 Å2 / Biso min: 10.33 Å2
Refinement stepCycle: LAST / Resolution: 1.953→43.414 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4833 0 56 246 5135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084971
X-RAY DIFFRACTIONf_angle_d1.0776736
X-RAY DIFFRACTIONf_chiral_restr0.071787
X-RAY DIFFRACTIONf_plane_restr0.005879
X-RAY DIFFRACTIONf_dihedral_angle_d13.4311818
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9535-1.99110.34231370.266826102747100
1.9911-2.03170.28371460.244726262772100
2.0317-2.07590.29491470.222425852732100
2.0759-2.12420.24161600.21526092769100
2.1242-2.17730.26431370.190426472784100
2.1773-2.23610.23111470.184626402787100
2.2361-2.30190.23781420.189826102752100
2.3019-2.37620.26471360.177226392775100
2.3762-2.46120.20051490.174526462795100
2.4612-2.55970.23381370.1826542791100
2.5597-2.67620.25591180.184626652783100
2.6762-2.81720.24321520.18426482800100
2.8172-2.99370.21671210.185326722793100
2.9937-3.22480.21831420.190226762818100
3.2248-3.54920.20211560.1762627278399
3.5492-4.06240.24071440.17562576272095
4.0624-5.11690.191330.1672464259790
5.1169-43.42440.22071340.20072688282293
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)
12.02381.49980.67972.86951.24131.79430.0153-0.0449-0.14810.08270.0785-0.35070.03380.1535-0.06030.18530.0162-0.0180.15630.00990.140315.197582.840928.8228
21.97740.7072-0.48610.82481.1656.9454-0.39360.25810.6915-0.87750.14690.707-0.4834-0.74590.19270.4694-0.0932-0.17030.30830.09550.464820.5255109.541324.3358
36.35594.9836-0.69074.5719-0.47991.5666-0.27740.38770.2805-0.39690.1994-0.0519-0.15970.25370.0460.2587-0.0285-0.00110.21370.03740.212416.399596.561521.7451
42.34380.9523-0.34223.19880.49122.60480.04180.1470.54110.07020.01930.1448-0.4986-0.1379-0.0570.2864-0.0163-0.03440.17240.01670.299119.6136109.795335.8833
52.8871-0.92550.07852.50250.20341.50640.0120.150.204-0.14130.0491-0.2856-0.07770.1717-0.05830.2067-0.04570.0280.1651-0.00390.141715.283481.5267-0.4165
60.1471-0.1695-0.05157.14930.88827.1156-0.0001-0.4294-0.15620.5783-0.03080.25890.5067-0.22770.05930.20650.0418-0.020.39580.0590.295826.452857.03955.4401
72.8331-1.3484-1.88132.24520.94352.1932-0.0116-0.1771-0.1088-0.12690.0223-0.0702-0.01520.039-0.02010.1933-0.0119-0.00570.13180.02520.151818.490466.6195-3.9608
82.0451-0.43-0.32443.7953-1.09024.9447-0.02-0.1164-0.4962-0.3260.0595-0.02480.792-0.1554-0.03620.33580.03510.02360.20180.03940.331826.305349.6833-5.551
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 80 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 140 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 141 through 187 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 188 through 343 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 4 through 80 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 81 through 151 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 152 through 245 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 246 through 342 )B0

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