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- PDB-2qjw: CRYSTAL STRUCTURE OF A PUTATIVE HYDROLASE OF THE ALPHA/BETA SUPER... -

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Database: PDB / ID: 2qjw
TitleCRYSTAL STRUCTURE OF A PUTATIVE HYDROLASE OF THE ALPHA/BETA SUPERFAMILY (XCC1541) FROM XANTHOMONAS CAMPESTRIS PV. CAMPESTRIS AT 1.35 A RESOLUTION
ComponentsUncharacterized protein XCC1541
KeywordsHYDROLASE / PUTATIVE HYDROLASE OF THE ALPHA/BETA SUPERFAMILY / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / L(+)-TARTARIC ACID / Uncharacterized protein
Function and homology information
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein XCC1541 (NP_636912.1) from Xanthomonas campestris at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF FOUR CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein XCC1541
B: Uncharacterized protein XCC1541
C: Uncharacterized protein XCC1541
D: Uncharacterized protein XCC1541
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,88218
Polymers75,7414
Non-polymers1,14114
Water13,818767
1
A: Uncharacterized protein XCC1541
B: Uncharacterized protein XCC1541
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,34010
Polymers37,8712
Non-polymers4698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-67 kcal/mol
Surface area14410 Å2
MethodPISA
2
C: Uncharacterized protein XCC1541
D: Uncharacterized protein XCC1541
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5428
Polymers37,8712
Non-polymers6726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-27 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.800, 60.640, 74.720
Angle α, β, γ (deg.)90.000, 94.570, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: ARG / End label comp-ID: LEU / Refine code: 5 / Auth seq-ID: 3 - 175 / Label seq-ID: 4 - 176

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Uncharacterized protein XCC1541


Mass: 18935.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Species: Xanthomonas campestris / Strain: NCPPB 528, LMG 568 / Gene: NP_636912.1, XCC1541 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8PAE4

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Non-polymers , 5 types, 781 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 767 / 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: 2.14 Å3/Da / Density % sol: 42.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: NANODROP, 0.264M Di-ammonium tartrate, 15.8% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 3, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97921
ReflectionResolution: 1.35→29.775 Å / Num. obs: 140150 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.984 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 10.76
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.35-1.40.5081.5457212686693.9
1.4-1.450.4461.7413032372395.8
1.45-1.520.3642.1493812843396.4
1.52-1.60.2772.8465392676696.7
1.6-1.70.2063.7467002689597.5
1.7-1.830.1435.4467662692798.2
1.83-2.020.0849.1486222812998.7
2.02-2.310.04615.5467722706599
2.31-2.910.02923.6482742741799.3
2.91-29.7750.01540.8488602721798.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→29.775 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.211 / SU ML: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.064
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CHLORIDE IONS, TARTRATE ION AND THE FRAGMENTS OF POLYETHYLENE GLYCOL 400 MOLECULE WITH DIFFERENT MOLECULAR WEIGHT WERE MODELED IN THIS STRUCTURE. 4. RESIDUES 71 TO 75 IN SUBUNIT D ARE DISORDERED AND NOT MODELED IN THE STRUCTURE. 5. UNEXPLAINED ELECTRON DENSITY NEAR RESIDUES A147 AND D147 ARE NOT MODELED. THEY ARE SUGGESTED AS NITROBENZENE (NBZ).
RfactorNum. reflection% reflectionSelection details
Rfree0.216 7030 5 %RANDOM
Rwork0.182 ---
obs0.184 140130 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.979 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20.26 Å2
2--0.47 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.35→29.775 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5138 0 65 767 5970
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0215564
X-RAY DIFFRACTIONr_bond_other_d0.0030.023709
X-RAY DIFFRACTIONr_angle_refined_deg1.7671.9767605
X-RAY DIFFRACTIONr_angle_other_deg1.12439049
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2515748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.40222.44209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.01915859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.91549
X-RAY DIFFRACTIONr_chiral_restr0.0750.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026378
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021116
X-RAY DIFFRACTIONr_nbd_refined0.2210.31266
X-RAY DIFFRACTIONr_nbd_other0.1930.34240
X-RAY DIFFRACTIONr_nbtor_refined0.1750.52805
X-RAY DIFFRACTIONr_nbtor_other0.0920.52926
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.5967
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1150.325
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.3124
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2240.578
X-RAY DIFFRACTIONr_mcbond_it1.90633716
X-RAY DIFFRACTIONr_mcbond_other0.92631460
X-RAY DIFFRACTIONr_mcangle_it2.61555817
X-RAY DIFFRACTIONr_scbond_it3.98982039
X-RAY DIFFRACTIONr_scangle_it5.57111788
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A908MEDIUM POSITIONAL0.270.5
2B908MEDIUM POSITIONAL0.290.5
3C908MEDIUM POSITIONAL0.220.5
4D908MEDIUM POSITIONAL0.210.5
1A911LOOSE POSITIONAL0.465
2B911LOOSE POSITIONAL0.495
3C911LOOSE POSITIONAL0.455
4D911LOOSE POSITIONAL0.375
1A908MEDIUM THERMAL1.842
2B908MEDIUM THERMAL1.352
3C908MEDIUM THERMAL1.652
4D908MEDIUM THERMAL1.852
1A911LOOSE THERMAL2.4110
2B911LOOSE THERMAL1.9210
3C911LOOSE THERMAL2.1810
4D911LOOSE THERMAL2.3110
LS refinement shellResolution: 1.35→1.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 534 -
Rwork0.337 9712 -
obs-10246 98.6 %

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