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- PDB-4jwp: Crystal structure of Ribosomal-protein-alanine N-acetyltransferas... -

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Basic information

Entry
Database: PDB / ID: 4jwp
TitleCrystal structure of Ribosomal-protein-alanine N-acetyltransferase from Brucella melitensis in complex with Acetyl CoA
ComponentsGCN5-related N-acetyltransferase
KeywordsTRANSFERASE / SSGCID / Ribosomal-protein-alanine N-acetyltransferase / Acetyl CoA / Coenzyme A / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / metal ion binding
Similarity search - Function
Acetyltransferase (GNAT) domain / 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
ACETYL COENZYME *A / GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Ribosomal-protein-alanine N-acetyltransferase from Brucella melitensis in complex with Acetyl CoA
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Arakaki, T. / Lorimer, D. / Edwards, T.E.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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: GCN5-related N-acetyltransferase
B: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2908
Polymers41,2852
Non-polymers1,0056
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-57 kcal/mol
Surface area14970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.420, 74.380, 67.550
Angle α, β, γ (deg.)90.000, 91.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GCN5-related N-acetyltransferase


Mass: 20642.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: 2308 / Gene: BAB1_1664 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2YRK4, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Microlytics MCSG1, C7: 200mM CaCl2, 100mM Tris pH 8.5, 25% PEG 4000G 3350, BrabA.17352.a.A1.PS01094 at 20mg/ml, 2.5mM CoA, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 15, 2012
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 24280 / Num. obs: 24170 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 26.445 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 27.17
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2-2.050.3015.7432631348195.4
2.05-2.110.2887.640211489199.2
2.11-2.170.25110.46535316871100
2.17-2.240.20213.1589516111100
2.24-2.310.22812.8954961552199.9
2.31-2.390.1981550521489199.5
2.39-2.480.14517.04544814771100
2.48-2.580.12818.51534314381100
2.58-2.70.10721.5850961369199.9
2.7-2.830.08625.18491213121100
2.83-2.980.07328.45468012481100
2.98-3.160.06732.49432811791100
3.16-3.380.04842.33428311401100
3.38-3.650.0452.16384810311100
3.65-40.03660.4836039681100
4-4.470.03366.953164857199.9
4.47-5.160.03266.828527711100
5.16-6.320.03757.7223826481100
6.32-8.940.0316219075151100
8.94-500.02779.05965282199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.36 Å
Translation3.5 Å19.36 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native structure, pdb entry 4J3G

4j3g


Resolution: 2→41.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.2248 / WRfactor Rwork: 0.1728 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8538 / SU B: 7.336 / SU ML: 0.11 / SU R Cruickshank DPI: 0.177 / SU Rfree: 0.1624 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 1232 5.1 %RANDOM
Rwork0.1728 ---
all0.1754 24280 --
obs0.1754 22938 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.73 Å2 / Biso mean: 24.201 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å2-0.22 Å2
2--0.58 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 56 303 2875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0192624
X-RAY DIFFRACTIONr_bond_other_d0.0010.022477
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.9723571
X-RAY DIFFRACTIONr_angle_other_deg0.73435634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35323.333123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.40115406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9181523
X-RAY DIFFRACTIONr_chiral_restr0.0850.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023027
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02641
X-RAY DIFFRACTIONr_mcbond_it0.9551.0861313
X-RAY DIFFRACTIONr_mcbond_other0.9521.0861312
X-RAY DIFFRACTIONr_mcangle_it1.5551.6211637
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 88 -
Rwork0.185 1620 -
all-1708 -
obs-1709 95.42 %
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)
10.28120.11390.18171.1395-0.1190.92790.0493-0.0497-0.02830.0307-0.0073-0.00310.0464-0.0543-0.0420.12190.0224-0.05440.02460.00720.060922.07935.93813.044
21.8828-0.2211.25040.33740.19612.6126-0.1728-0.3150.1758-0.03290.0367-0.0186-0.3693-0.27750.13610.19130.0559-0.08050.0583-0.03590.093617.68964.34119.189
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 164
2X-RAY DIFFRACTION1A201 - 204
3X-RAY DIFFRACTION2B2 - 164
4X-RAY DIFFRACTION2B201 - 202

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