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- PDB-4lq8: Rickettsia rickettsii cell surface antigen 4 (sca4) head domain (... -

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Basic information

Entry
Database: PDB / ID: 4lq8
TitleRickettsia rickettsii cell surface antigen 4 (sca4) head domain (residues 21-360)
ComponentsSca-family protein
KeywordsCELL ADHESION
Function / homologyRickettsia surface antigen, 120kDa / 120 KDa Rickettsia surface antigen / cytoplasm / Antigenic heat-stable 120 kDa protein / 120 kDa antigen
Function and homology information
Biological speciesRickettsia rickettsii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsLee, J.H. / Vonrhein, C. / Bricogne, G. / Izard, T.
CitationJournal: Protein Sci. / Year: 2013
Title: Crystal structure of the N-terminal domains of the surface cell antigen 4 of Rickettsia.
Authors: Lee, J.H. / Vonrhein, C. / Bricogne, G. / Izard, T.
History
DepositionJul 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sca-family protein
B: Sca-family protein


Theoretical massNumber of molelcules
Total (without water)75,3482
Polymers75,3482
Non-polymers00
Water4,666259
1
A: Sca-family protein


Theoretical massNumber of molelcules
Total (without water)37,6741
Polymers37,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Sca-family protein


Theoretical massNumber of molelcules
Total (without water)37,6741
Polymers37,6741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.152, 98.152, 155.526
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Sca-family protein


Mass: 37673.852 Da / Num. of mol.: 2 / Fragment: UNP residues 38-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia rickettsii (bacteria) / Gene: sca4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: E3T8S6, UniProt: B0BXR4*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.8M sodium malonate (pH 6), 5% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 40961 / % possible obs: 95.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.92 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 16.2

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Processing

SoftwareName: BUSTER / Version: 2.13.0 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→49.08 Å / Cor.coef. Fo:Fc: 0.9459 / Cor.coef. Fo:Fc free: 0.9331 / SU R Cruickshank DPI: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 2050 5 %RANDOM
Rwork0.1781 ---
obs0.1799 40960 95.24 %-
Displacement parametersBiso mean: 37.63 Å2
Baniso -1Baniso -2Baniso -3
1--2.2878 Å20 Å20 Å2
2---2.2878 Å20 Å2
3---4.5757 Å2
Refine analyzeLuzzati coordinate error obs: 0.251 Å
Refinement stepCycle: LAST / Resolution: 2.2→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4628 0 0 259 4887
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014715HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.086361HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1699SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes659HARMONIC5
X-RAY DIFFRACTIONt_it4715HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion16.23
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion639SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies2HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5561SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2676 132 4.52 %
Rwork0.2209 2790 -
all0.223 2922 -
obs--95.24 %
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)
11.586-0.7415-0.28220.75450.20451.09270.0032-0.0019-0.11770.0106-0.06120.1275-0.0143-0.02050.058-0.1504-0.00450.0038-0.1164-0.0413-0.158822.290365.316521.993
21.2116-0.41390.21220.7068-0.11441.2963-0.0059-0.03430.107-0.04210.00520.0005-0.08930.05640.0008-0.0997-0.0205-0.0182-0.15390.0006-0.17318.777631.7394-9.6116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|49 - A|360 }A49 - 360
2X-RAY DIFFRACTION2{ B|49 - B|359 }B49 - 359

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