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- PDB-2ozh: Crystal structure of a putative acetyltransferase belonging to th... -

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Basic information

Entry
Database: PDB / ID: 2ozh
TitleCrystal structure of a putative acetyltransferase belonging to the gnat family (xcc2953) from xanthomonas campestris pv. campestris at 1.40 A resolution
ComponentsHypothetical protein XCC2953
KeywordsTRANSFERASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
: / Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of hypothetical protein (NP_638301.1) from Xanthomonas campestris at 1.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 26, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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_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
Revision 1.5Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
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

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Assembly

Deposited unit
A: Hypothetical protein XCC2953
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4789
Polymers15,9761
Non-polymers5028
Water4,486249
1
A: Hypothetical protein XCC2953
hetero molecules

A: Hypothetical protein XCC2953
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,95618
Polymers31,9512
Non-polymers1,00516
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_565-x,-y+3/2,z1
Buried area7030 Å2
ΔGint-35 kcal/mol
Surface area14790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.957, 101.957, 101.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-143-

SO4

21A-143-

SO4

31A-523-

HOH

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Components

#1: Protein Hypothetical protein XCC2953


Mass: 15975.532 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Species: Xanthomonas campestris / Strain: NCPPB528, LMG568 / Gene: NP_638301.1, XCC2953 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8P6L4
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: NANODROP, 1.6M (NH4)2SO4, 0.1M Bicine pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97898, 0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 11, 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
20.978981
30.97921
ReflectionResolution: 1.4→29.437 Å / Num. obs: 34768 / % possible obs: 100 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 5.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.4-1.447.30.5921.31853825340.592100
1.44-1.487.30.4581.71812824710.458100
1.48-1.527.40.3941.91801324460.394100
1.52-1.577.40.3212.31729023460.321100
1.57-1.627.40.2622.91674522650.262100
1.62-1.677.40.2193.41657722370.219100
1.67-1.747.40.1854.11566921090.185100
1.74-1.817.40.1544.81529820570.154100
1.81-1.897.40.1275.61466919750.127100
1.89-1.987.50.1036.61397418730.103100
1.98-2.097.40.0946.91340218010.094100
2.09-2.217.40.0887.41263917010.088100
2.21-2.377.40.0877.41182315960.087100
2.37-2.567.40.0827.71108815010.082100
2.56-2.87.40.078.81009713610.07100
2.8-3.137.50.06110.1951812760.061100
3.13-3.617.40.05311.2811310970.053100
3.61-4.437.40.05211.470019490.052100
4.43-6.267.30.05410.454557510.054100
6.26-29.446.70.05610.628334220.05699

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SOLVEphasing
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.4→29.437 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.398 / SU ML: 0.028 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.047
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SO4 AND EDO WERE MODELED BASED ON CRYSTALLIZATION AND CRYO CONDITIONS. 5. THE N-TERMINAL GLYCINE (0) IS PARTIALLY COVALENTLY MODIFIED. THE MODIFICATION IS MODELED AS UNKNOWN LIGAND, UNL. THE IDENTITY OF THE MODIFIED AMINO ACID IS LIKELY ACETYL-GLYCINE.
RfactorNum. reflection% reflectionSelection details
Rfree0.155 1744 5 %RANDOM
Rwork0.143 ---
all0.143 ---
obs0.143 34667 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.021 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.437 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1110 0 33 249 1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221272
X-RAY DIFFRACTIONr_bond_other_d0.0010.021164
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9761743
X-RAY DIFFRACTIONr_angle_other_deg0.8732703
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1335171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47821.55258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.99315197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9451512
X-RAY DIFFRACTIONr_chiral_restr0.090.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021456
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02296
X-RAY DIFFRACTIONr_nbd_refined0.2260.2221
X-RAY DIFFRACTIONr_nbd_other0.1890.21158
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2628
X-RAY DIFFRACTIONr_nbtor_other0.0920.2758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2165
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.229
X-RAY DIFFRACTIONr_mcbond_it1.5743784
X-RAY DIFFRACTIONr_mcbond_other0.3363310
X-RAY DIFFRACTIONr_mcangle_it2.26751246
X-RAY DIFFRACTIONr_scbond_it3.5348543
X-RAY DIFFRACTIONr_scangle_it4.69211484
LS refinement shellResolution: 1.4→1.437 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 115 -
Rwork0.228 2336 -
obs-2451 96.72 %
Refinement TLS params.Method: refined / Origin x: 11.091 Å / Origin y: 71.658 Å / Origin z: 11.765 Å
111213212223313233
T-0.0343 Å2-0.004 Å20.0029 Å2--0.0081 Å2-0.0117 Å2---0.0225 Å2
L0.6537 °20.0105 °20.1185 °2-0.2902 °2-0.045 °2--0.2613 °2
S-0.0055 Å °0.0736 Å °-0.0537 Å °-0.0251 Å °0.0111 Å °-0.0009 Å °0.0317 Å °0.0264 Å °-0.0056 Å °
Refinement TLS groupSelection: ALL

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