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- PDB-5cjj: The crystal structure of phosphoribosylglycinamide formyltransfer... -

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Basic information

Entry
Database: PDB / ID: 5cjj
TitleThe crystal structure of phosphoribosylglycinamide formyltransferase from Campylobacter jejuni subsp. jejuni NCTC 11168
ComponentsPhosphoribosylglycinamide formyltransferase
KeywordsTRANSFERASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


phosphoribosylglycinamide formyltransferase 1 / phosphoribosylglycinamide formyltransferase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
Phosphoribosylglycinamide formyltransferase / Formyl transferase, N-terminal domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni serotype O:2 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.42 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: The crystal structure of phosphoribosylglycinamide formyltransferase from Campylobacter jejuni subsp. jejuni NCTC 11168
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJul 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylglycinamide formyltransferase
B: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7197
Polymers43,2932
Non-polymers4265
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-46 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.162, 65.162, 368.905
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphoribosylglycinamide formyltransferase / / 5'-phosphoribosylglycinamide transformylase / GAR transformylase


Mass: 21646.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni serotype O:2 (strain NCTC 11168) (Campylobacter)
Strain: NCTC 11168 / Gene: purN, Cj0187c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: Q0PBV2, phosphoribosylglycinamide formyltransferase 1

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Non-polymers , 5 types, 52 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1M HEPES, 30% v/v Jeffamine ED-2001Reagent

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924, 0.97937
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2012
RadiationMonochromator: Silicon 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979241
20.979371
ReflectionResolution: 2.42→50 Å / Num. all: 19055 / Num. obs: 19055 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 15.2 % / Biso Wilson estimate: 26.97 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 28.4
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3.2 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.42→50 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2896 850 4.96 %Random selection
Rwork0.2494 ---
obs0.2515 17130 90.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.42→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 24 47 2965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022964
X-RAY DIFFRACTIONf_angle_d0.6663998
X-RAY DIFFRACTIONf_dihedral_angle_d13.2521066
X-RAY DIFFRACTIONf_chiral_restr0.047472
X-RAY DIFFRACTIONf_plane_restr0.003500
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4161-2.56740.3649720.32331523X-RAY DIFFRACTION52
2.5674-2.76560.44371450.34042546X-RAY DIFFRACTION88
2.7656-3.04390.37741540.33182920X-RAY DIFFRACTION99
3.0439-3.48430.29661510.28482965X-RAY DIFFRACTION100
3.4843-4.38930.27991660.21193035X-RAY DIFFRACTION100
4.3893-48.14530.2171620.20223291X-RAY DIFFRACTION100
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)
14.9688-0.07060.00490.65210.22730.2975-0.44180.1491-0.37340.19120.35580.15540.0649-0.26250.10470.6678-0.13260.24890.568-0.15790.38327.229224.212624.3153
23.6978-0.9036-2.51576.22472.4076.5469-1.2089-0.6712-0.98411.17040.8571-0.35011.56790.46740.16191.00170.29690.30180.5751-0.02170.598215.246519.512832.8878
34.88581.84010.46431.6171-0.96633.6937-0.5533-0.77270.25721.01220.5198-0.44550.5691.2880.08620.86910.369-0.09561.1046-0.29370.671920.053130.227338.6252
45.17440.7956-0.02113.82671.75956.0443-0.6624-0.94770.67741.21180.4914-0.16690.60080.9070.13350.71120.10920.08970.5484-0.23380.562110.709333.002337.7855
51.10650.3976-0.41151.17160.02951.0372-0.3447-0.1297-0.22430.15910.03770.10720.2526-0.19180.00130.6608-0.00970.28320.2673-0.10820.44563.11431.169438.5131
61.88560.8807-0.73090.4157-0.40831.4491-0.2784-0.0902-0.5562-0.37160.0724-0.40190.29640.1880.29950.7965-0.07760.39350.3367-0.10680.5525-3.453616.432347.692
70.858-0.3875-0.85660.64970.47691.9508-0.1665-0.0978-0.178-0.0230.101-0.07370.36160.33250.64951.312-0.07590.77410.4994-0.09761.03813.203811.893939.6468
83.97340.34761.59931.94740.64932.86780.5032-0.1121-0.7013-0.0759-0.27130.23821.2612-0.0967-0.4560.8358-0.18640.05560.3312-0.13930.3833-28.7297-5.263161.0364
93.8731-0.73882.79358.3224-0.63535.73280.19230.2924-0.2749-0.3895-0.10980.11450.39360.0009-0.0450.5245-0.13130.04110.3672-0.1210.3669-30.9373-0.530348.342
101.76920.6110.33662.33061.73054.06460.1936-0.0595-0.06750.1778-0.62440.48250.3148-0.99140.27830.5906-0.21670.07650.4474-0.2020.3992-37.0682.758458.4092
110.4932-0.15730.15171.2370.7480.67620.1792-0.08550.208-0.1417-0.0491-0.0185-0.066-0.01380.2790.7112-0.21980.11750.2158-0.10860.3961-25.913911.110858.095
121.64021.2051-0.02563.8545-0.25380.99870.07160.11840.1958-0.78060.1992-0.014-0.26070.122-0.01380.8118-0.24920.21070.3187-0.11030.4486-16.837512.990447.2316
131.44751.50970.12673.24571.32621.4364-0.20340.3435-0.0389-0.74730.3852-0.27780.15710.076-0.15750.8804-0.25190.13030.3715-0.14850.3518-21.44983.432546.2015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 8 )
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 53 )
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 98 )
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 111 )
6X-RAY DIFFRACTION6chain 'A' and (resid 112 through 163 )
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 188 )
8X-RAY DIFFRACTION8chain 'B' and (resid -1 through 9 )
9X-RAY DIFFRACTION9chain 'B' and (resid 10 through 23 )
10X-RAY DIFFRACTION10chain 'B' and (resid 24 through 83 )
11X-RAY DIFFRACTION11chain 'B' and (resid 84 through 122 )
12X-RAY DIFFRACTION12chain 'B' and (resid 123 through 163 )
13X-RAY DIFFRACTION13chain 'B' and (resid 164 through 188 )

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