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- PDB-3hiu: The crystal structure of protein (XCC3681) from Xanthomonas campe... -

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Basic information

Entry
Database: PDB / ID: 3hiu
TitleThe crystal structure of protein (XCC3681) from Xanthomonas campestris pv. campestris str. ATCC 33913
ComponentsUncharacterized protein
KeywordsStructural Genomics / unknown function / APC40011 / XCC3681 / Xanthomonas campestris pv. campestris str. ATCC 33913 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homologyProtein of unknown function DUF892, YciF-like / Domain of unknown function (DUF892) / Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsTan, K. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of protein (XCC3681) from Xanthomonas campestris pv. campestris str. ATCC 33913
Authors: Tan, K. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,94325
Polymers75,7964
Non-polymers1,14721
Water5,945330
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,68916
Polymers37,8982
Non-polymers79114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-12 kcal/mol
Surface area14240 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2549
Polymers37,8982
Non-polymers3567
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-28 kcal/mol
Surface area15000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.592, 56.843, 53.990
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein


Mass: 18949.039 Da / Num. of mol.: 4 / Fragment: sequence database residues 5-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: XCC3681 / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8P4M6
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 293 K
Details: 0.1M K Thiocyanate, 30% PEG2KMME, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 5, 2009 / Details: MIRROR
RadiationMonochromator: SI 111 CRYSTAL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.488
ReflectionResolution: 1.85→50 Å / Num. obs: 52443 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 18.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.807 / Mean I/σ(I) obs: 1.14 / % possible all: 97.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→49.72 Å / σ(F): 1.89 / Stereochemistry target values: TWIN_LSQ_F
Details: THE AUTHORS STATE THAT THE CRYSTAL WAS TREATED AS A MEROHEDRAL TWIN. THE REFINEMENT WAS PERFORMED WITH AN APPLICATION OF A TWINNING OPERATOR (-H, -K, L) AND TWINNING FRACTION WAS REFINED TO ...Details: THE AUTHORS STATE THAT THE CRYSTAL WAS TREATED AS A MEROHEDRAL TWIN. THE REFINEMENT WAS PERFORMED WITH AN APPLICATION OF A TWINNING OPERATOR (-H, -K, L) AND TWINNING FRACTION WAS REFINED TO 0.488. THE STRUCTURE WAS SOLVED IN SPACE GROUP P212121. FOR THE REFINEMENT PURPOSE THE SPACE GROUP WAS REDUCED FROM P212121 TO P21.
RfactorNum. reflection% reflection
Rfree0.257 5228 5.22 %
Rwork0.207 --
obs0.21 52354 96.4 %
all-100236 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80.78 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.7152 Å20 Å21.1213 Å2
2--9.1241 Å2-0 Å2
3---1.9468 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4664 0 72 330 5066
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064774
X-RAY DIFFRACTIONf_angle_d0.9516396
X-RAY DIFFRACTIONf_dihedral_angle_d18.6651803
X-RAY DIFFRACTIONf_chiral_restr0.067715
X-RAY DIFFRACTIONf_plane_restr0.003833
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.88320.38022650.35573992X-RAY DIFFRACTION98
1.8832-1.91750.35632440.33054723X-RAY DIFFRACTION98
1.9175-1.95440.35612670.33094808X-RAY DIFFRACTION98
1.9544-1.99420.32792750.30874861X-RAY DIFFRACTION98
1.9942-2.03760.30712440.28984870X-RAY DIFFRACTION98
2.0376-2.0850.312300.29354957X-RAY DIFFRACTION98
2.085-2.13710.27712770.2864866X-RAY DIFFRACTION98
2.1371-2.19490.28992690.26144888X-RAY DIFFRACTION98
2.1949-2.25950.23712240.25354968X-RAY DIFFRACTION98
2.2595-2.33250.29442620.254833X-RAY DIFFRACTION98
2.3325-2.41580.24692660.24084852X-RAY DIFFRACTION98
2.4158-2.51250.28372260.2264899X-RAY DIFFRACTION98
2.5125-2.62690.30172590.22434913X-RAY DIFFRACTION98
2.6269-2.76540.27412560.22314813X-RAY DIFFRACTION98
2.7654-2.93860.27652700.20524851X-RAY DIFFRACTION98
2.9386-3.16550.25732560.18864783X-RAY DIFFRACTION98
3.1655-3.48390.22482630.16974675X-RAY DIFFRACTION98
3.4839-3.98790.21252300.14044562X-RAY DIFFRACTION98
3.9879-5.02360.19692650.14144482X-RAY DIFFRACTION98
5.0236-49.7390.26072410.19914551X-RAY DIFFRACTION98
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.8299-0.02350.69360.37720.09581.83810.0088-0.46360.07270.0819-0.003-0.0274-0.0584-0.1130.00360.1463-0.01280.010.2216-0.00970.15062.6346-4.4758-32.4501
21.0764-0.23870.32810.2795-0.10261.95880.07480.41010.062-0.1219-0.11520.0472-0.110.19610.02160.10630.0076-0.0012-0.0056-0.0360.0559
30.7264-0.2656-0.2440.2536-0.3561.937-0.0274-0.39490.00440.0610.0053-0.06450.0969-0.05560.00560.1968-0.01740.00690.236-0.02440.2297
40.7837-0.1465-0.0719-0.31170.19162.2266-0.05580.142-0.05820.02910.01370.05040.07550.0260.02910.2075-0.00170.00150.1585-0.01830.3022
Refinement TLS groupSelection details: CHAIN D

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