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- PDB-4n27: X-ray structure of Brucella abortus RicA -

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Basic information

Entry
Database: PDB / ID: 4n27
TitleX-ray structure of Brucella abortus RicA
ComponentsBacterial transferase hexapeptide repeat
KeywordsTRANSFERASE / gamma carbonic anhydrase / Zinc binding
Function / homology
Function and homology information


transferase activity / metal ion binding
Similarity search - Function
: / : / Hexapeptide repeat / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Bacterial transferase hexapeptide repeat
Similarity search - Component
Biological speciesBrucella Abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsHerrou, J. / Crosson, S.
CitationJournal: Biochemistry / Year: 2013
Title: Molecular Structure of the Brucella abortus Metalloprotein RicA, a Rab2-Binding Virulence Effector.
Authors: Herrou, J. / Crosson, S.
History
DepositionOct 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_conn.ptnr2_label_seq_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: Bacterial transferase hexapeptide repeat
B: Bacterial transferase hexapeptide repeat
C: Bacterial transferase hexapeptide repeat
D: Bacterial transferase hexapeptide repeat
E: Bacterial transferase hexapeptide repeat
F: Bacterial transferase hexapeptide repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,49118
Polymers124,7086
Non-polymers2,78312
Water32418
1
A: Bacterial transferase hexapeptide repeat
B: Bacterial transferase hexapeptide repeat
C: Bacterial transferase hexapeptide repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7469
Polymers62,3543
Non-polymers1,3926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9070 Å2
ΔGint-133 kcal/mol
Surface area18640 Å2
MethodPISA
2
D: Bacterial transferase hexapeptide repeat
E: Bacterial transferase hexapeptide repeat
F: Bacterial transferase hexapeptide repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7469
Polymers62,3543
Non-polymers1,3926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-132 kcal/mol
Surface area18600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.430, 57.440, 127.610
Angle α, β, γ (deg.)90.00, 91.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Bacterial transferase hexapeptide repeat


Mass: 20784.682 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella Abortus (bacteria) / Strain: 2308 / Gene: BAB1_1279, BruAb1_1263 / Plasmid: pET28c / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q2YQG1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 3.01 Å3/Da / Density % sol: 59.12 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100 mM Sodium Acetate, pH 4.6, 25 % (w/v) PEG 1000, 200 mM NaCl, 30 mM Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 28, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.7→63.77 Å / Num. obs: 39871 / % possible obs: 100 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1
Reflection shellResolution: 2.7→2.7983 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
xia2data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→63.77 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 28.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2545 2004 5.03 %
Rwork0.2057 --
obs0.2082 39871 99.78 %
all-40748 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.73→63.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7818 0 141 18 7977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118127
X-RAY DIFFRACTIONf_angle_d1.39310977
X-RAY DIFFRACTIONf_dihedral_angle_d13.5912997
X-RAY DIFFRACTIONf_chiral_restr0.0541212
X-RAY DIFFRACTIONf_plane_restr0.0071422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.79830.3111340.27752663X-RAY DIFFRACTION100
2.7983-2.87390.32131560.2762667X-RAY DIFFRACTION100
2.8739-2.95850.31971340.25242669X-RAY DIFFRACTION100
2.9585-3.0540.32171460.24272681X-RAY DIFFRACTION100
3.054-3.16310.27821430.23222665X-RAY DIFFRACTION100
3.1631-3.28980.27271530.22112683X-RAY DIFFRACTION100
3.2898-3.43950.29451370.22912709X-RAY DIFFRACTION100
3.4395-3.62080.28781510.21672683X-RAY DIFFRACTION100
3.6208-3.84770.24281470.20052702X-RAY DIFFRACTION100
3.8477-4.14470.23151450.20152714X-RAY DIFFRACTION100
4.1447-4.56170.2551520.18932697X-RAY DIFFRACTION100
4.5617-5.22150.22641350.17082751X-RAY DIFFRACTION100
5.2215-6.57750.23011360.19692760X-RAY DIFFRACTION100
6.5775-63.78950.19331350.17342823X-RAY DIFFRACTION99

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