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- PDB-4dim: Crystal structure of phosphoribosylglycinamide synthetase from An... -

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Basic information

Entry
Database: PDB / ID: 4dim
TitleCrystal structure of phosphoribosylglycinamide synthetase from Anaerococcus prevotii
ComponentsPhosphoribosylglycinamide synthetase
KeywordsLIGASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


ligase activity / ATP binding / metal ion binding
Similarity search - Function
Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Rossmann fold - #20 / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Rossmann fold / 2-Layer Sandwich ...Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Rossmann fold - #20 / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoribosylglycinamide synthetase
Similarity search - Component
Biological speciesAnaerococcus prevotii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å
AuthorsMichalska, K. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of phosphoribosylglycinamide synthetase from Anaerococcus prevotii
Authors: Michalska, K. / Wu, R. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionJan 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylglycinamide synthetase


Theoretical massNumber of molelcules
Total (without water)45,8041
Polymers45,8041
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.270, 84.467, 49.642
Angle α, β, γ (deg.)90.00, 100.54, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphoribosylglycinamide synthetase


Mass: 45803.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaerococcus prevotii (bacteria) / Strain: DSM 20548 / Gene: Apre_1268 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Magic / References: UniProt: C7RDM8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-Tris/HCl, 20% PEG MME 5000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97904 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97904 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 15596 / Num. obs: 15567 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 100.03 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 24.4
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 2.35 / Num. unique all: 747 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
Auto-Rickshawphasing
SHELXmodel building
ABSmodel building
HELICAPmodel building
BUCCANEERmodel building
Cootmodel building
BUSTER2.10.0refinement
HKL-3000data reduction
HKL-3000data scaling
SHELXphasing
MLPHAREphasing
DMphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.61→48.8 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.9341 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 901 5.81 %random
Rwork0.1837 ---
all0.1865 15514 --
obs0.1865 15514 99.77 %-
Displacement parametersBiso mean: 104.6 Å2
Baniso -1Baniso -2Baniso -3
1--10.2944 Å20 Å29.9054 Å2
2---12.7848 Å20 Å2
3---23.0792 Å2
Refine analyzeLuzzati coordinate error obs: 0.484 Å
Refinement stepCycle: LAST / Resolution: 2.61→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3091 0 0 2 3093
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0126263HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2311399HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1827SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes103HARMONIC2
X-RAY DIFFRACTIONt_gen_planes875HARMONIC5
X-RAY DIFFRACTIONt_it6263HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion3.41
X-RAY DIFFRACTIONt_chiral_improper_torsion426SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6614SEMIHARMONIC4
LS refinement shellResolution: 2.61→2.79 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3039 165 5.91 %
Rwork0.2143 2628 -
all0.2198 2793 -
obs-2793 99.77 %
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)
15.59760.8571.41531.05970.31554.2523-0.15660.63460.5003-0.40080.07370.4668-0.528-0.43550.08290.01970.0371-0.1509-0.19110.0723-0.04256.33643.308930.2027
26.1484-0.7483-2.82642.40542.82114.62980.05330.3050.55610.3573-0.0452-0.1232-0.53240.6103-0.0081-0.0406-0.15180.01240.304-0.015-0.308541.71241.786832.8631
37.09753.3027-2.19478.3154-1.93397.3023-0.05420.2338-0.3809-0.4208-0.09240.15470.34360.28950.1465-0.30130.16830.12250.304-0.0735-0.258544.3704-11.10326.4582
44.32570.0426-1.18040.85960.89664.0222-0.07060.05350.0691-0.3567-0.17650.08-0.43930.56350.2471-0.0649-0.0105-0.0087-0.13530.0128-0.276527.1605-2.000139.6225
55.29341.1891-0.19971.7802-0.31234.4073-0.0792-0.52620.3233-0.0177-0.04140.1445-0.24790.28010.1207-0.02450.01980.0037-0.1452-0.0645-0.182518.8939-0.870947.1736
65.7432.66563.20235.2021.58412.06030.05160.0984-0.2821-0.56150.07890.34220.3138-0.3871-0.13060.0448-0.0753-0.0615-0.1914-0.03450.12635.5926-26.133342.7835
74.91152.26281.22738.31541.1683.6126-0.21020.1826-0.4714-0.63030.03810.43630.41410.15070.1721-0.1050.05410.0038-0.24540.0559-0.06259.0271-21.549144.7143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|3 - 107}A3 - 107
2X-RAY DIFFRACTION2{A|108 - 146}A108 - 146
3X-RAY DIFFRACTION3{A|147 - 176}A147 - 176
4X-RAY DIFFRACTION4{A|177 - 215}A177 - 215
5X-RAY DIFFRACTION5{A|216 - 324}A216 - 324
6X-RAY DIFFRACTION6{A|325 - 347}A325 - 347
7X-RAY DIFFRACTION7{A|348 - 400}A348 - 400

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