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- PDB-1xfj: Crystal structure of protein CC_0490 from Caulobacter crescentus,... -

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Basic information

Entry
Database: PDB / ID: 1xfj
TitleCrystal structure of protein CC_0490 from Caulobacter crescentus, Pfam DUF152
Componentsconserved hypothetical protein
Keywordsstructural genomics / unknown function / Protein structure initiative (PSI) / Hypothetical protein / alpha-beta-beta-alpha / two-domain structure / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


2'-deoxyadenosine deaminase activity / S-methyl-5-thioadenosine phosphorylase activity / adenosine deaminase activity / metal ion binding
Similarity search - Function
CNF1/YfiH-like putative cysteine hydrolases / CNF1/YfiH-like putative cysteine hydrolases / Multi-copper polyphenol oxidoreductase / Multi-copper polyphenol oxidoreductase superfamily / Multi-copper polyphenol oxidoreductase laccase / Cytotoxic necrotizing factor-like, catalytic / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / BETA-MERCAPTOETHANOL / Purine nucleoside phosphorylase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsKrishnamurthy, N.R. / Kumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a conserved hypothetical protein from Caulobacter crescentus
Authors: Krishnamurthy, N.R. / Kumaran, D. / Swaminathan, S.
History
DepositionSep 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_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

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Assembly

Deposited unit
A: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3774
Polymers28,1481
Non-polymers2293
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.807, 66.828, 43.17
Angle α, β, γ (deg.)90, 110.6, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein conserved hypothetical protein


Mass: 28148.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AAV3
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#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.: 253 / 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 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: PEG 4000, Sodium-acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792, 0.9797, 0.94
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Aug 14, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
20.97971
30.941
ReflectionResolution: 1.75→50 Å / Num. all: 21008 / Num. obs: 21008 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.125 / Num. unique all: 1760 / % possible all: 81.4

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Processing

Software
NameClassification
CBASSdata collection
HKL-2000data reduction
SOLVEphasing
SHARPphasing
ARP/wARPmodel building
CNSrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Ser 38 and Asp 113 are in the disallowed region of the Ramachandran plot. This seems to be the characteristic feature of this protein. It is observed in the other related entries as well. ...Details: Ser 38 and Asp 113 are in the disallowed region of the Ramachandran plot. This seems to be the characteristic feature of this protein. It is observed in the other related entries as well. The electron density was absent for the missing residues listed in remark 465.
RfactorNum. reflectionSelection details
Rfree0.22 1631 RANDOM
Rwork0.18 --
all-20832 -
obs-20832 -
Displacement parametersBiso mean: 9.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.043 Å20 Å20.219 Å2
2---0.32 Å20 Å2
3---0.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1935 0 14 253 2202
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.3
LS refinement shellResolution: 1.75→1.83 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.24 180 -
Rwork0.185 --
obs-2297 86.8 %

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