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- PDB-3c8v: Crystal structure of putative acetyltransferase (YP_390128.1) fro... -

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Basic information

Entry
Database: PDB / ID: 3c8v
TitleCrystal structure of putative acetyltransferase (YP_390128.1) from Desulfovibrio desulfuricans G20 at 2.28 A resolution
ComponentsPutative acetyltransferase
KeywordsTRANSFERASE / YP_390128.1 / Putative acetyltransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


transferase activity / metal ion binding
Similarity search - Function
Helix Hairpins - #2050 / Hexapeptide repeat including loop / Hexapeptide repeat including loop / Single helix bin / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Trimeric LpxA-like superfamily / Helix Hairpins / 3 Solenoid / Single alpha-helices involved in coiled-coils or other helix-helix interfaces ...Helix Hairpins - #2050 / Hexapeptide repeat including loop / Hexapeptide repeat including loop / Single helix bin / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Trimeric LpxA-like superfamily / Helix Hairpins / 3 Solenoid / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Hexapeptide repeat-containing transferase
Similarity search - Component
Biological speciesDesulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.28 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative acetyltransferase (YP_390128.1) from Desulfovibrio desulfuricans G20 at 2.28 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 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 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 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: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative acetyltransferase
B: Putative acetyltransferase
C: Putative acetyltransferase
D: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,43545
Polymers223,2474
Non-polymers2,18841
Water9,728540
1
A: Putative acetyltransferase
B: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,89125
Polymers111,6232
Non-polymers1,26823
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
MethodPISA
2
C: Putative acetyltransferase
D: Putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,54320
Polymers111,6232
Non-polymers92018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.617, 249.617, 104.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D

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
11GLYGLYLYSLYS2AA0 - 9019 - 109
21GLYGLYLYSLYS2BB0 - 9019 - 109
31GLYGLYLYSLYS2CC0 - 9019 - 109
41GLYGLYLYSLYS2DD0 - 9019 - 109
52ARGARGGLUGLU6AA91 - 109110 - 128
62ARGARGGLUGLU6BB91 - 109110 - 128
72ARGARGGLUGLU6CC91 - 109110 - 128
82ARGARGGLUGLU6DD91 - 109110 - 128
93VALVALASNASN2AA110 - 475129 - 494
103VALVALASNASN2BB110 - 475129 - 494
113VALVALASNASN2CC110 - 475129 - 494
123VALVALASNASN2DD110 - 475129 - 494

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Components

#1: Protein
Putative acetyltransferase


Mass: 55811.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfovibrio desulfuricans subsp. desulfuricans str. (bacteria)
Species: Desulfovibrio desulfuricans / Strain: G20 / Gene: YP_390128.1, Dde_3640 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q30V63
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 2.82 Å3/Da / Density % sol: 56.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: NANODROP, 0.2M K Formate, 20.0% PEG 3350, No Buffer pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0000, 0.9795, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 15, 2007
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
30.97971
ReflectionResolution: 2.28→48.057 Å / Num. obs: 105055 / % possible obs: 94.6 % / Observed criterion σ(I): -3 / Redundancy: 2.75 % / Biso Wilson estimate: 41.55 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.28-2.362.090.4462.115353735267.6
2.36-2.460.4072.5251431078391.9
2.46-2.570.3553.2303011077099
2.57-2.70.2844.1301761051698.6
2.7-2.870.1975.8318961109298.9
2.87-3.090.1258.7315561094198.5
3.09-3.40.07413.8314021091298.3
3.4-3.890.03922.8313941088897.8
3.89-4.890.02630.9310051081597.3
4.89-48.0570.02234.5310891098597.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.28→48.057 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 13.379 / SU ML: 0.162 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.26 / ESU R Free: 0.204
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. EDO AND CL WERE MODELED BASED ON CRYSTALLIZATION CONDITIONS. MG WAS TENTATIVELY MODELED BASED ON ENVIRONMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.223 5271 5 %RANDOM
Rwork0.18 ---
obs0.182 105052 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.479 Å2
Baniso -1Baniso -2Baniso -3
1--0.86 Å2-0.43 Å20 Å2
2---0.86 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.28→48.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14264 0 125 540 14929
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02114699
X-RAY DIFFRACTIONr_bond_other_d0.0020.029897
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.94419835
X-RAY DIFFRACTIONr_angle_other_deg1.571324036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63351839
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29724.052686
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.725152362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2251574
X-RAY DIFFRACTIONr_chiral_restr0.0740.22154
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216533
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023073
X-RAY DIFFRACTIONr_mcbond_it1.26239112
X-RAY DIFFRACTIONr_mcbond_other0.43533787
X-RAY DIFFRACTIONr_mcangle_it2.386514612
X-RAY DIFFRACTIONr_scbond_it4.30585587
X-RAY DIFFRACTIONr_scangle_it6.434115218
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2523TIGHT POSITIONAL0.210.2
2B2523TIGHT POSITIONAL0.180.2
3C2523TIGHT POSITIONAL0.140.2
4D2523TIGHT POSITIONAL0.130.2
1A2940MEDIUM POSITIONAL0.280.5
2B2940MEDIUM POSITIONAL0.340.5
3C2940MEDIUM POSITIONAL0.230.5
4D2940MEDIUM POSITIONAL0.230.5
1A181LOOSE POSITIONAL0.865
2B181LOOSE POSITIONAL0.685
3C181LOOSE POSITIONAL0.75
4D181LOOSE POSITIONAL0.635
1A2523TIGHT THERMAL0.812
2B2523TIGHT THERMAL0.732
3C2523TIGHT THERMAL0.62
4D2523TIGHT THERMAL0.662
1A2940MEDIUM THERMAL0.964
2B2940MEDIUM THERMAL0.864
3C2940MEDIUM THERMAL0.734
4D2940MEDIUM THERMAL0.794
1A181LOOSE THERMAL2.2310
2B181LOOSE THERMAL1.9910
3C181LOOSE THERMAL1.5610
4D181LOOSE THERMAL1.7110
LS refinement shellResolution: 2.28→2.344 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 282 -
Rwork0.265 5367 -
all-5649 -
obs--69.54 %
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)
11.2767-0.1324-0.59610.41690.03571.213-0.16080.1501-0.2793-0.11010.09030.05630.1672-0.19650.0705-0.2578-0.05010.0326-0.16320.0485-0.1446147.5858138.277566.2043
23.06731.1328-0.61221.1477-0.29150.884-0.08520.4086-0.05720.0696-0.0063-0.07170.1497-0.03770.0915-0.2296-0.11410.09430.03260.03-0.1155105.9226113.918690.5057
31.95460.3570.50711.33520.151.84220.1678-0.28280.02390.625-0.18560.5430.2043-0.33920.01780.2138-0.09180.3550.0897-0.02130.023115.2932143.2927126.2309
40.99620.24780.22711.4187-0.07241.37680.0187-0.03470.48770.18950.01440.234-0.4865-0.2498-0.033-0.110.14680.0602-0.09330.07940.0465135.0474175.153186.7762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 47519 - 494
2X-RAY DIFFRACTION2BB0 - 47519 - 494
3X-RAY DIFFRACTION3CC0 - 47519 - 494
4X-RAY DIFFRACTION4DD0 - 47519 - 494

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