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- PDB-2rjb: Crystal structure of uncharacterized protein YdcJ (SF1787) from S... -

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Basic information

Entry
Database: PDB / ID: 2rjb
TitleCrystal structure of uncharacterized protein YdcJ (SF1787) from Shigella flexneri which includes domain DUF1338. Northeast Structural Genomics Consortium target SfR276
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Uncharacterized protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Uncharacterised protein PF07063, DUF1338 / Domain of unknown function DUF1338 / Domain of unknown function (DUF1338), C-terminal / DUF1338 / 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
DUF1338 domain-containing protein / DUF1338 domain-containing protein
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsSeetharaman, J. / Chen, Y. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Chen, Y. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of uncharacterized protein YdcJ (SF1787) from Shigella flexneri which includes domain DUF1338.
Authors: Seetharaman, J. / Chen, Y. / Wang, D. / Fang, Y. / Cunningham, K. / Ma, L.-C. / Xia, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,1208
Polymers210,8584
Non-polymers2624
Water9,044502
1
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7802
Polymers52,7151
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7802
Polymers52,7151
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7802
Polymers52,7151
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7802
Polymers52,7151
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)192.209, 76.387, 159.052
Angle α, β, γ (deg.)90.00, 116.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Uncharacterized protein


Mass: 52714.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Strain: 301 / Serotype 2a / Gene: S1487, SF1787 / Plasmid: pET21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q83KU0, UniProt: A0A0H2UZX2*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.48 Å3/Da / Density % sol: 50.34 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 7
Details: NH4H2PO4, 0.1M MOPS, 20% PEG 1000, pH 7.0, MICROBATCH UNDER OIL, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 10, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 64525 / Num. obs: 64525 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 31.2 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.066 / Net I/σ(I): 11.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 10 / Num. unique all: 12337 / Rsym value: 0.275 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→41.12 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 108028.4 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3238 3 %RANDOM
Rwork0.233 ---
obs0.233 61527 87 %-
all-62160 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.9052 Å2 / ksol: 0.313935 e/Å3
Displacement parametersBiso mean: 45.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.72 Å20 Å210.16 Å2
2---3.49 Å20 Å2
3---1.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12721 0 4 502 13227
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it3.162.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 413 2.9 %
Rwork0.277 13878 -
obs--68.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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