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- PDB-4j7o: Structure of the N-terminal Repeat Domain of Rickettsia Sca2 -

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Basic information

Entry
Database: PDB / ID: 4j7o
TitleStructure of the N-terminal Repeat Domain of Rickettsia Sca2
ComponentsPutative surface cell antigen sca2
KeywordsCELL INVASION / Helical repeat / actin nucleation / actin
Function / homology: / Surface cell antigen Sca2 helical repeat / Autotransporter beta-domain / Autotransporter beta-domain / Autotransporter beta-domain profile. / Autotransporter beta-domain / Autotransporter beta-domain superfamily / cell outer membrane / Putative surface cell antigen sca2
Function and homology information
Biological speciesRickettsia conorii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.175 Å
AuthorsMadasu, Y. / Dominguez, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Rickettsia Sca2 has evolved formin-like activity through a different molecular mechanism.
Authors: Madasu, Y. / Suarez, C. / Kast, D.J. / Kovar, D.R. / Dominguez, R.
History
DepositionFeb 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative surface cell antigen sca2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4856
Polymers42,0241
Non-polymers4605
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.020, 102.870, 55.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Putative surface cell antigen sca2


Mass: 42024.055 Da / Num. of mol.: 1 / Fragment: N-terminal Repeat Domain, UNP residues 34-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia conorii (bacteria) / Gene: sca2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q92JF7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.76 Å3/Da / Density % sol: 55.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M sodium citrate, 18-20% (w/v) PEG 3350 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9769 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2011 / Details: Bent, triangular Si(111) monochromator crystal
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9769 Å / Relative weight: 1
ReflectionResolution: 2.175→64 Å / Num. all: 25180 / Num. obs: 24526 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.83 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 13.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.175→64 Å / SU ML: 0.21 / σ(F): 0 / Phase error: 24.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 1927 8.16 %Random
Rwork0.179 ---
all0.1829 25180 --
obs0.1829 23613 93.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.2 Å2
Baniso -1Baniso -2Baniso -3
1-6.188 Å20 Å20 Å2
2--22.4 Å20 Å2
3----28.588 Å2
Refinement stepCycle: LAST / Resolution: 2.175→64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2661 0 30 109 2800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042760
X-RAY DIFFRACTIONf_angle_d0.7183717
X-RAY DIFFRACTIONf_dihedral_angle_d14.8081091
X-RAY DIFFRACTIONf_chiral_restr0.051403
X-RAY DIFFRACTIONf_plane_restr0.002484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.175-2.22930.364800.294887795754
2.2293-2.28960.28011320.26541447157989
2.2896-2.3570.33431250.25381502162793
2.357-2.4330.33551340.23061509164394
2.433-2.520.28171400.2291543168394
2.52-2.62090.26041380.21771561169996
2.6209-2.74020.29221400.21211604174497
2.7402-2.88470.24691410.21491573171498
2.8847-3.06540.24991480.20641630177899
3.0654-3.30210.27091460.198816441790100
3.3021-3.63430.21831460.180916501796100
3.6343-4.16010.19821480.139416681816100
4.1601-5.2410.19421510.136316951846100
5.241-64.15860.17451580.16391783194199
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)
19.7510.9958-0.61334.9106-0.07737.33020.1137-1.01850.64050.49580.06040.2958-0.2303-0.4318-0.18720.4071-0.03730.00160.6161-0.00220.432912.363828.397367.937
26.0833-3.1602-2.43136.56323.26496.1910.2292-0.1758-0.7202-0.1442-0.08940.30.5756-0.124-0.11330.4188-0.0774-0.13820.40780.11520.382525.758115.931258.1072
35.9485-0.9835-0.18038.1304-2.09896.73390.1698-0.0044-0.05860.1552-0.3109-0.11250.19560.34360.15730.3112-0.0223-0.02870.34950.02530.367340.130525.375854.6033
44.4175-2.2911.09819.5285-4.42415.12580.2290.265-0.1491-0.442-0.18340.00640.38830.0918-0.01240.3510.0231-0.00920.27880.00390.288634.796624.054448.4055
56.8263-5.05921.47838.5824-2.10394.1110.24690.2549-0.508-0.5689-0.29140.33140.78270.19170.01230.51110.08260.03850.34170.03140.374524.068636.021834.8553
61.9486-3.4439-1.37933.22882.26172.3496-0.1858-0.0809-0.3077-0.23390.12270.28770.31640.27220.09550.48360.0091-0.01150.36260.10620.480412.864752.930230.1795
78.7011-6.0928-4.8548.82514.03957.56240.4840.6935-0.1285-0.5789-0.5694-0.0484-0.1134-0.14970.0330.39920.0518-0.06760.34410.03640.36522.393969.399131.9727
85.5345-1.2088-4.48776.84654.70739.03340.38030.2340.5093-0.2142-0.56360.3243-0.8596-0.60030.25070.46720.0657-0.12320.3309-0.03970.5537-9.404381.50141.7317
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 34:72)
2X-RAY DIFFRACTION2chain 'A' and (resseq 73:121)
3X-RAY DIFFRACTION3chain 'A' and (resseq 122:164)
4X-RAY DIFFRACTION4chain 'A' and (resseq 165:196)
5X-RAY DIFFRACTION5chain 'A' and (resseq 197:238)
6X-RAY DIFFRACTION6chain 'A' and (resseq 239:281)
7X-RAY DIFFRACTION7chain 'A' and (resseq 282:321)
8X-RAY DIFFRACTION8chain 'A' and (resseq 322:362)

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