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- PDB-2pbz: Crystal structure of an IMP biosynthesis protein PurP from Thermo... -

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Basic information

Entry
Database: PDB / ID: 2pbz
TitleCrystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis
ComponentsHypothetical protein
KeywordsLIGASE / NYSGXRC / PSI-II / IMP biosynthesis / ATP binding protein / PurP / 10188d / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


IMP biosynthetic process / ligase activity, forming carbon-nitrogen bonds / magnesium ion binding / ATP binding
Similarity search - Function
IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily ...IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Uncharacterized protein
Similarity search - Component
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an IMP biosynthesis protein PurP from Thermococcus kodakaraensis
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,2766
Polymers109,7553
Non-polymers1,5223
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-65 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.342, 87.400, 175.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hypothetical protein


Mass: 36584.984 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Strain: KOD1 / Gene: PurP, TK0431 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL
References: UniProt: Q5JD28, Ligases; Forming carbon-nitrogen bonds; Other carbon-nitrogen ligases
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.52 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 0.2M NaCl, 0.1M Na-acetate, 30% MPD, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K, pH 4.60

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONNSLS X29A10.9792
SYNCHROTRONNSLS X12C20.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 16, 2007 / Details: MIRRORS
RadiationMonochromator: SI(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 33174 / % possible obs: 94.7 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 25.5 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 12.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1 / % possible all: 68.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→31 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 90726.93 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
Details: 1. Restrained NCS was used during refinement due to paucity of data. 2. Residual density in the final difference map was modeled as ATP molecule. 3. Residues listed as missing in remark 465 ...Details: 1. Restrained NCS was used during refinement due to paucity of data. 2. Residual density in the final difference map was modeled as ATP molecule. 3. Residues listed as missing in remark 465 were not modeled because of lack of electron density. 4. Outliers for Ramachandran plot were due to poor electron density except for His11 of all chains. The electron density for His 11 is well defined.
RfactorNum. reflection% reflectionSelection details
Rfree0.3 733 2.5 %RANDOM
Rwork0.276 ---
obs0.276 29269 84.5 %-
all-33174 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.7504 Å2 / ksol: 0.294838 e/Å3
Displacement parametersBiso mean: 55.3 Å2
Baniso -1Baniso -2Baniso -3
1-8.68 Å20 Å20 Å2
2---4.42 Å20 Å2
3----4.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.44 Å
Refinement stepCycle: LAST / Resolution: 2.5→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7083 0 93 240 7416
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.08
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.048 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.391 65 2.4 %
Rwork0.332 2590 -
obs--46.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMATP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ATP.PARAM

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