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- PDB-4s1n: The crystal structure of phosphoribosylglycinamide formyltransfer... -

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Basic information

Entry
Database: PDB / ID: 4s1n
TitleThe crystal structure of phosphoribosylglycinamide formyltransferase from Streptococcus pneumoniae TIGR4
ComponentsPhosphoribosylglycinamide formyltransferase
KeywordsTRANSFERASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
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
Phosphoribosylglycinamide formyltransferase / Phosphoribosylglycinamide formyltransferase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of phosphoribosylglycinamide formyltransferase from Streptococcus pneumoniae TIGR4
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionJan 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7404
Polymers20,6341
Non-polymers1063
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.206, 46.227, 91.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. It is predicted to be monomeric.

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Components

#1: Protein Phosphoribosylglycinamide formyltransferase


Mass: 20633.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: purN, SP_0048 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q97TA1, UniProt: A0A0H2UKZ6*PLUS, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16M Calcium Acetate, 0.08M Sodium Cacodylate:HCl, 14.4%(w/v) PEG8000, 20% (v/v)Glycerol, pH 6.5, 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2014 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→41.3 Å / Num. all: 5384 / Num. obs: 5384 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 9.6 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.142 / Net I/σ(I): 14.03
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.57 / Num. unique all: 262 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDBuilder/HKL3000phasing
MLPHAREBuilder/HKL3000phasing
DMBuilder/HKL3000model building
DENZOBuilder/HKL3000data reduction
SCALEPACKBuilder/HKL3000data scaling
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMBuilder/HKL3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→41.3 Å / SU ML: 0.41 / σ(F): 1.37 / Phase error: 25.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2758 262 5.09 %random
Rwork0.2004 ---
obs0.2041 5145 95.45 %-
all-5145 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1392 0 3 4 1399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0011424
X-RAY DIFFRACTIONf_angle_d0.4851935
X-RAY DIFFRACTIONf_dihedral_angle_d9.439504
X-RAY DIFFRACTIONf_chiral_restr0.03216
X-RAY DIFFRACTIONf_plane_restr0.002251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6968-3.39740.34931190.24162291X-RAY DIFFRACTION92
3.3974-41.2330.2471430.18242592X-RAY DIFFRACTION99
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)
14.9878-3.91153.68087.8246-8.72552.0383-0.2517-0.5516-0.76611.36210.1918-0.8972-2.30480.10770.3670.5363-0.0382-0.14260.4531-0.04290.6478-1.9724.3902-5.6231
28.1312-3.88813.90393.9815-4.03517.18420.3346-0.7525-0.79150.68020.442-0.623-1.6014-0.8351-0.02060.4180.0726-0.10660.3891-0.00780.4101-5.107312.8583-6.0901
37.6182-4.43972.14127.022.4797.7422-0.008-0.04370.67440.3597-0.0339-0.8249-0.0027-0.6806-0.02870.3001-0.0310.00570.34360.03390.43831.80238.814-12.5208
42.66750.6863-0.90787.92227.98.71620.063-0.0093-0.0195-0.20610.222-0.97340.14540.4701-0.21870.35660.0285-0.01190.38070.06980.4864.7251-4.5141-14.8476
53.98962.1442-2.04918.53152.49052.993-0.0897-0.1983-0.37020.3113-0.0448-0.10890.3783-0.43930.15650.4298-0.01860.02380.34810.06050.3539-5.1218-3.8954-8.0391
66.8122-1.30773.00595.7114-1.65313.32960.05690.5167-0.3378-0.81620.52671.1897-0.0297-0.2986-0.49390.5078-0.0485-0.07050.54270.00810.5616-22.54813.4312-14.4362
79.1075-5.4574-1.07714.72723.84497.1607-0.0222.4186-2.02011.1751-1.65742.34721.7258-2.04491.99850.6761-0.14320.26040.9951-0.42731.2414-15.517-7.8873-8.8266
83.2684-1.9956-1.89873.42062.28631.6753-0.01660.5033-0.0392-0.7101-0.22191.6116-0.43730.1640.6030.6248-0.1097-0.20070.6747-0.01210.6649-24.997310.385-11.1171
99.3168-2.24815.85424.3490.99855.0860.16340.1014-0.3371-0.08760.2290.34680.44370.2088-0.13180.5417-0.0380.09870.4215-0.04080.4006-15.431911.3461-7.5934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 12 )
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 21 )
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 43 )
4X-RAY DIFFRACTION4chain 'A' and (resid 44 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 102 )
6X-RAY DIFFRACTION6chain 'A' and (resid 103 through 132 )
7X-RAY DIFFRACTION7chain 'A' and (resid 133 through 141 )
8X-RAY DIFFRACTION8chain 'A' and (resid 142 through 155 )
9X-RAY DIFFRACTION9chain 'A' and (resid 156 through 180 )

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