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- PDB-4ds3: Crystal Structure of Phosphoribosylglycinamide formyltransferase ... -

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Basic information

Entry
Database: PDB / ID: 4ds3
TitleCrystal Structure of Phosphoribosylglycinamide formyltransferase from Brucella melitensis
ComponentsPhosphoribosylglycinamide formyltransferase
KeywordsTRANSFERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Phosphoribosylglycinamide formyltransferase
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 / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / 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
Similarity search - Component
Biological speciesBrucella melitensis bv. 1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Phosphoribosylglycinamide formyltransferase from Brucella melitensis
Authors: Fairman, J.W. / Gardberg, A.S. / Staker, B.L. / Stewart, L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)22,4266
Polymers22,0101
Non-polymers4165
Water2,972165
1
A: Phosphoribosylglycinamide formyltransferase
hetero molecules

A: Phosphoribosylglycinamide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,85212
Polymers44,0212
Non-polymers83110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4140 Å2
ΔGint-112 kcal/mol
Surface area16450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.595, 134.063, 56.663
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-402-

HOH

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Components

#1: Protein Phosphoribosylglycinamide formyltransferase


Mass: 22010.480 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis bv. 1 (bacteria) / Strain: 16M / ATCC 23456 / NCTC 10094
Gene: BAWG_0970, BMEI1241, Phosphoribosylglycinamide formyltransferase
Production host: Escherichia coli (E. coli)
References: UniProt: Q8YGB8, phosphoribosylglycinamide formyltransferase 1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2.0 M ammonium sulfate, 200 mM sodium chloride, 100 mM sodium cacodylate pH 6.50, BrmeA.01059.a.A1 PS01278 81.6 mg/ml, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 17663 / Num. obs: 17663 / % possible obs: 95.7 % / Observed criterion σ(F): 2.05 / Observed criterion σ(I): 2.05 / Redundancy: 3.1 % / Rmerge(I) obs: 0.071 / Χ2: 1.009 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.921.90.31217311.035195.2
1.92-1.992.20.21917340.981196.7
1.99-2.082.30.15617681.032196.5
2.08-2.192.70.13117691.016196.8
2.19-2.332.80.1217221.008194.5
2.33-2.513.20.09617890.989197.9
2.51-2.763.60.08718050.996198.4
2.76-3.164.10.07818301.015198.4
3.16-3.993.80.06317040.994190.6
3.99-504.30.05818111.026192

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TQR

3tqr


Resolution: 1.85→50 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.668 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2315 906 5.1 %RANDOM
Rwork0.184 ---
all0.1865 17629 --
obs0.1865 17629 95.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 61.18 Å2 / Biso mean: 26.936 Å2 / Biso min: 8.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1407 0 22 165 1594
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191457
X-RAY DIFFRACTIONr_angle_refined_deg2.0941.9921976
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.18422.77854
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32415228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3391511
X-RAY DIFFRACTIONr_chiral_restr0.1410.2234
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211079
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.468 56 -
Rwork0.372 1112 -
all-1168 -
obs--92.11 %
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)
12.5369-0.3145-1.7297.45871.05131.275-0.1206-0.2946-0.07060.34070.0876-0.10560.11660.1930.0330.07640.02280.01960.12230.01040.08210.28812.157236.9841
21.6742-1.16640.95563.9437-0.26050.61810.06690.0334-0.04120.0338-0.08410.19270.03450.03740.01720.0512-0.00740.00970.04710.01110.06348.16188.293726.8235
30.9902-0.5459-0.1051.50210.67270.9783-0.068-0.0594-0.00590.03970.06230.12610.0325-0.03580.00570.0222-0.0070.01130.0173-0.00230.03534.590121.498933.7037
40.89850.1912-0.66170.33220.03413.71720.014-0.02450.1323-0.0063-0.0059-0.0265-0.028-0.0006-0.00810.00920.00610.0010.0124-0.00270.04919.637421.455416.9411
53.96968.0105-0.761916.2362-0.62314.4303-0.05680.14110.3257-0.23290.28770.577-1.3193-0.0539-0.23080.2453-0.00520.0670.2617-0.01290.428120.870527.22629.0009
61.1383-0.4075-0.41990.91440.06220.1655-0.030.0368-0.02910.04460.02250.07390.0111-0.01630.00750.0616-0.0239-0.00740.0626-0.00280.068119.714911.631816.8046
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 9
2X-RAY DIFFRACTION2A10 - 28
3X-RAY DIFFRACTION3A29 - 104
4X-RAY DIFFRACTION4A105 - 141
5X-RAY DIFFRACTION5A142 - 150
6X-RAY DIFFRACTION6A151 - 204

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