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- PDB-2a7w: Crystal Structure of Phosphoribosyl-ATP Pyrophosphatase from Chro... -

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Basic information

Entry
Database: PDB / ID: 2a7w
TitleCrystal Structure of Phosphoribosyl-ATP Pyrophosphatase from Chromobacterium violaceum (ATCC 12472). NESG TARGET CVR7
ComponentsPhosphoribosyl-ATP pyrophosphatase
KeywordsHYDROLASE / PHOSPHORIBOSYL-ATP PYROPHOSPHATASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG
Function / homology
Function and homology information


phosphoribosyl-ATP diphosphatase / phosphoribosyl-ATP diphosphatase activity / L-histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoribosyl-ATP pyrophosphohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase / MazG-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphoribosyl-ATP pyrophosphatase
Similarity search - Component
Biological speciesChromobacterium violaceum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsBenach, J. / Forouhar, F. / Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Phosphoribosyl-ATP Pyrophosphatase from Chromobacterium violaceum. NESG Target CVR7.
Authors: Benach, J. / Forouhar, F. / Kuzin, A.P. / Abashidze, M. / Vorobiev, S.M. / Rong, X. / Acton, T.B. / Montelione, G.T. / Hunt, J.F.
History
DepositionJul 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosyl-ATP pyrophosphatase
B: Phosphoribosyl-ATP pyrophosphatase
C: Phosphoribosyl-ATP pyrophosphatase
D: Phosphoribosyl-ATP pyrophosphatase
E: Phosphoribosyl-ATP pyrophosphatase
F: Phosphoribosyl-ATP pyrophosphatase
G: Phosphoribosyl-ATP pyrophosphatase
H: Phosphoribosyl-ATP pyrophosphatase
I: Phosphoribosyl-ATP pyrophosphatase
J: Phosphoribosyl-ATP pyrophosphatase
K: Phosphoribosyl-ATP pyrophosphatase
L: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)161,02412
Polymers161,02412
Non-polymers00
Water6,107339
1
A: Phosphoribosyl-ATP pyrophosphatase
B: Phosphoribosyl-ATP pyrophosphatase
C: Phosphoribosyl-ATP pyrophosphatase
D: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)53,6754
Polymers53,6754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10090 Å2
ΔGint-84 kcal/mol
Surface area15680 Å2
MethodPISA
2
E: Phosphoribosyl-ATP pyrophosphatase
F: Phosphoribosyl-ATP pyrophosphatase
G: Phosphoribosyl-ATP pyrophosphatase
H: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)53,6754
Polymers53,6754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-85 kcal/mol
Surface area15670 Å2
MethodPISA
3
I: Phosphoribosyl-ATP pyrophosphatase
J: Phosphoribosyl-ATP pyrophosphatase
K: Phosphoribosyl-ATP pyrophosphatase
L: Phosphoribosyl-ATP pyrophosphatase


Theoretical massNumber of molelcules
Total (without water)53,6754
Polymers53,6754
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-84 kcal/mol
Surface area15690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.938, 67.544, 113.512
Angle α, β, γ (deg.)90.00, 92.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphoribosyl-ATP pyrophosphatase / PRA-PH


Mass: 13418.668 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium violaceum (bacteria) / Gene: hisE / Production host: Escherichia coli (E. coli)
References: UniProt: Q7P0E6, phosphoribosyl-ATP diphosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.575 Å3/Da / Density % sol: 52.29 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908 / Wavelength: 0.97908,0.97933,0.96771
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979081
20.979331
30.967711
ReflectionResolution: 2.8→30 Å / Num. all: 36861 / Num. obs: 36861 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.07 % / Biso Wilson estimate: 133.8 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 17.63
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 2.53 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.8→29.31 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1612598.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2799 1800 5 %RANDOM
Rwork0.2582 ---
obs0.2582 35928 97.5 %-
all-35928 --
Solvent computationBsol: 19.4752 Å2 / ksol: 0.275387 e/Å3
Displacement parametersBiso mean: 56.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.93 Å20 Å23.6 Å2
2---2.45 Å20 Å2
3---12.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.57 Å0.48 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8736 0 0 339 9075
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.141.5
X-RAY DIFFRACTIONc_mcangle_it3.782
X-RAY DIFFRACTIONc_scbond_it3.282
X-RAY DIFFRACTIONc_scangle_it5.492.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.407 293 4.9 %
Rwork0.355 5662 -
obs--98 %
Xplor fileSerial no: 1 / Topol file: PROTEIN.TOP

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