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- PDB-1vqr: Crystal structure of a virulence factor (cj0248) from campylobact... -

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Basic information

Entry
Database: PDB / ID: 1vqr
TitleCrystal structure of a virulence factor (cj0248) from campylobacter jejuni subsp. jejuni at 2.25 A resolution
Componentshypothetical protein Cj0248
KeywordsUNKNOWN FUNCTION / Hd-domain/pdease-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


: / Metal-dependent hydrolase HDOD / HDOD domain / HD-related output (HDOD) domain profile. / Hypothetical protein af1432 / Hypothetical protein af1432 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HDOD domain-containing protein / :
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni NCTC 11168 (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of virulence factor CJ0248 from Campylobacter jejuni at 2.25 A resolution reveals a new fold.
Authors: Xu, Q. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. ...Authors: Xu, Q. / Schwarzenbacher, R. / McMullan, D. / Abdubek, P. / Agarwalla, S. / Ambing, E. / Axelrod, H. / Biorac, T. / Canaves, J.M. / Chiu, H.J. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Hornsby, M. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Miller, M.D. / Moy, K. / Nigoghossian, E. / Paulsen, J. / Quijano, K. / Reyes, R. / Rife, C. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / White, A. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionDec 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.6Oct 9, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF ... BIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY (SEC) AND MULTI-ANGLE LIGHT SCATTERING (MALS) SUPPORT THE ASSIGNMENT OF THE BIOLOGICAL OLIGOMERIZATION STATE AS A MONOMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein Cj0248
B: hypothetical protein Cj0248
C: hypothetical protein Cj0248
D: hypothetical protein Cj0248


Theoretical massNumber of molelcules
Total (without water)135,1474
Polymers135,1474
Non-polymers00
Water3,477193
1
A: hypothetical protein Cj0248


Theoretical massNumber of molelcules
Total (without water)33,7871
Polymers33,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: hypothetical protein Cj0248


Theoretical massNumber of molelcules
Total (without water)33,7871
Polymers33,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: hypothetical protein Cj0248


Theoretical massNumber of molelcules
Total (without water)33,7871
Polymers33,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: hypothetical protein Cj0248


Theoretical massNumber of molelcules
Total (without water)33,7871
Polymers33,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.141, 122.090, 96.897
Angle α, β, γ (deg.)90.00, 120.58, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D
331A
341B
351C
361D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11MSEMSEMSEMSE5AA1 - 513 - 17
21MSEMSEMSEMSE5BB517
31MSEMSEMSEMSE5CC1 - 513 - 17
41MSEMSEMSEMSE5DD517
52ASNASNTYRTYR2AA6 - 2918 - 41
62ASNASNTYRTYR2BB6 - 2918 - 41
72ASNASNTYRTYR2CC6 - 2918 - 41
82ASNASNTYRTYR2DD6 - 2918 - 41
93VALVALGLUGLU5AA30 - 3842 - 50
103VALVALGLUGLU5BB30 - 3842 - 50
113VALVALGLUGLU5CC30 - 3842 - 50
123VALVALGLUGLU5DD30 - 3842 - 50
134THRTHRALAALA2AA39 - 9251 - 104
144THRTHRALAALA2BB39 - 9251 - 104
154THRTHRALAALA2CC39 - 9251 - 104
164THRTHRALAALA2DD39 - 9251 - 104
175ASPASPASNASN5AA93 - 98105 - 110
185ASPASPASNASN5BB93 - 98105 - 110
195ASPASPASNASN5CC93 - 98105 - 110
205ASPASPASNASN5DD93 - 98105 - 110
216PHEPHELEULEU2AA99 - 170111 - 182
226PHEPHELEULEU2BB99 - 170111 - 182
236PHEPHELEULEU2CC99 - 170111 - 182
246PHEPHELEULEU2DD99 - 170111 - 182
257ASNASNASNASN5AA171 - 175183 - 187
267ASNASNASNASN5BB171 - 175183 - 187
277ASNASNASNASN5CC171 - 175183 - 187
287ASNASNASNASN5DD171 - 175183 - 187
298LEULEULYSLYS2AA176 - 255188 - 267
308LEULEULYSLYS2BB176 - 255188 - 267
318LEULEULYSLYS2CC176 - 255188 - 267
328LEULEULYSLYS2DD176 - 255188 - 267
339GLUGLUASNASN6AA256 - 280268 - 292
349GLUGLUASNASN6BB256 - 280268 - 292
359GLUGLUASNASN6CC256 - 280268 - 292
369GLUGLUASNASN6DD256 - 280268 - 292
DetailsBIOMOLECULE: 1, 2, 3, 4 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 4 CHAIN(S). SEE FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY (SEC) AND MULTI-ANGLE LIGHT SCATTERING (MALS) SUPPORT THE ASSIGNMENT OF THE BIOLOGICAL OLIGOMERIZATION STATE AS A MONOMER. GENERATING THE BIOMOLECULE COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. BIOMOLECULE: 1 APPLY THE FOLLOWING TO CHAINS: A BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 2 APPLY THE FOLLOWING TO CHAINS: B BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 3 APPLY THE FOLLOWING TO CHAINS: C BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 BIOMOLECULE: 4 APPLY THE FOLLOWING TO CHAINS: D BIOMT1 1 1.000000 0.000000 0.000000 0.00000 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 BIOMT3 1 0.000000 0.000000 1.000000 0.00000

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Components

#1: Protein
hypothetical protein Cj0248


Mass: 33786.750 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni NCTC 11168 (Campylobacter)
Species: Campylobacter jejuni / Strain: subsp. jejuni NCTC 11168 / Gene: Cj0248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9PIP7, UniProt: Q0PBQ7*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.58 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.5
Details: 20.0% PEG-6000, 1.0M LiCl, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.978956
DetectorType: ADSC / Detector: CCD / Date: Nov 11, 2004 / Details: fixed-height exit beam, toroidal focusing mirror
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978956 Å / Relative weight: 1
ReflectionResolution: 2.25→61.05 Å / Num. obs: 56900 / % possible obs: 97.4 % / Redundancy: 2.7 % / Biso Wilson estimate: 56.18 Å2 / Rsym value: 0.047 / Net I/σ(I): 11.4
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 3921 / Rsym value: 0.398 / % possible all: 90.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA4.2)data scaling
SHELXDphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.25→61.04 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.936 / SU B: 13.538 / SU ML: 0.167 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.216
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. UNINTERPRETED DENSITY: LOOPS A34-35, B33-36, D31-36, AND HIS TAG FOR CHAIN C. 3. SIZE EXCLUSION CHROMATOGRAPHY (SEC) AND MULTI-ANGLE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. UNINTERPRETED DENSITY: LOOPS A34-35, B33-36, D31-36, AND HIS TAG FOR CHAIN C. 3. SIZE EXCLUSION CHROMATOGRAPHY (SEC) AND MULTI-ANGLE LIGHT SCATTERING (MALS) SUPPORT THE ASSIGNMENT OF THE BIOLOGICAL OLIGOMERIZATION STATE AS A MONOMER
RfactorNum. reflection% reflectionSelection details
Rfree0.23286 2850 5 %RANDOM
Rwork0.19312 ---
obs0.19519 54049 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.549 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20.91 Å2
2---1.22 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.25→61.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8475 0 0 193 8668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228660
X-RAY DIFFRACTIONr_bond_other_d0.0020.028024
X-RAY DIFFRACTIONr_angle_refined_deg1.3551.96211783
X-RAY DIFFRACTIONr_angle_other_deg0.907318582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.17851092
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60825.489368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.482151447
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4911522
X-RAY DIFFRACTIONr_chiral_restr0.080.21418
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029562
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021636
X-RAY DIFFRACTIONr_nbd_refined0.2140.22087
X-RAY DIFFRACTIONr_nbd_other0.1660.27417
X-RAY DIFFRACTIONr_nbtor_other0.0880.24752
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2257
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1380.27
X-RAY DIFFRACTIONr_mcbond_it1.61635646
X-RAY DIFFRACTIONr_mcbond_other0.27832204
X-RAY DIFFRACTIONr_mcangle_it2.41558887
X-RAY DIFFRACTIONr_scbond_it4.52983364
X-RAY DIFFRACTIONr_scangle_it6.027112896
X-RAY DIFFRACTIONr_nbtor_refined0.1780.24382
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1362tight positional0.070.05
2B1362tight positional0.070.05
3C1362tight positional0.050.05
4D1362tight positional0.060.05
1A2106medium positional0.490.5
2B2106medium positional0.420.5
3C2106medium positional0.380.5
4D2106medium positional0.410.5
1A391loose positional0.565
2B391loose positional0.695
3C391loose positional0.625
4D391loose positional0.555
1A1362tight thermal0.170.5
2B1362tight thermal0.160.5
3C1362tight thermal0.160.5
4D1362tight thermal0.160.5
1A2106medium thermal0.962
2B2106medium thermal0.872
3C2106medium thermal0.872
4D2106medium thermal0.892
1A391loose thermal2.610
2B391loose thermal3.2210
3C391loose thermal3.0810
4D391loose thermal3.6110
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 203 5.18 %
Rwork0.255 3713 -
obs--90.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.93810.2025-0.01272.1733-0.2762.3260.0179-0.1259-0.04-0.0613-0.0490.16510.1619-0.13830.0311-0.1405-0.01480.0086-0.17570.0397-0.1668-42.80333.360223.4153
21.529-0.1886-0.26852.5495-0.9732.1859-0.0372-0.09540.03750.028-0.0198-0.0491-0.07820.10770.057-0.1407-0.0747-0.0241-0.01270.0608-0.1619-43.857211.349163.6358
33.2267-0.34550.24812.45340.69831.73350.0569-0.8022-0.17020.37940.09220.16950.25150.1157-0.1492-0.10590.0111-0.00020.02820.0581-0.0997-45.7027-10.780620.1252
43.380.35830.12174.2729-0.21541.13640.1183-0.37290.3621-0.0462-0.0647-0.0403-0.19070.0044-0.0536-0.1111-0.016-0.0089-0.1585-0.0922-0.1475-85.739110.785715.8128
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 28512 - 297
22BB5 - 28117 - 293
33CC1 - 28113 - 293
44DD5 - 28117 - 293

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