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- PDB-5d2r: Inhibitor Bound Cell Shape Determinant Protein Csd4 from Helicoba... -

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Basic information

Entry
Database: PDB / ID: 5d2r
TitleInhibitor Bound Cell Shape Determinant Protein Csd4 from Helicobacter pylori
ComponentsConserved hypothetical secreted protein
Keywordshydrolase/hydrolase inhibitor / mixed alpha beta sandwich / carboxypeptidase / M14 / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


D,L-carboxypeptidase, peptidase domain / Metallo-carboxypeptidase, C-terminal domain / Carboxypeptidase M99, beta-barrel domain / Carboxypeptidase controlling helical cell shape catalytic / C-terminal domain of metallo-carboxypeptidase / beta-barrel domain of carboxypeptidase M99
Similarity search - Domain/homology
Chem-56W / IODIDE ION / Conserved hypothetical secreted protein
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsChan, A.C. / Murphy, M.E.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: A Bacterial Cell Shape-Determining Inhibitor.
Authors: Liu, Y. / Frirdich, E. / Taylor, J.A. / Chan, A.C. / Blair, K.M. / Vermeulen, J. / Ha, R. / Murphy, M.E. / Salama, N.R. / Gaynor, E.C. / Tanner, M.E.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved hypothetical secreted protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,18224
Polymers50,1791
Non-polymers3,00423
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.840, 66.610, 144.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Conserved hypothetical secreted protein


Mass: 50178.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: G27 / Gene: HPG27_353 / Plasmid: pET15b(mod) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5ZAD9
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: I
#4: Chemical ChemComp-56W / (2R,6R)-2-{[(R)-[(3R)-3-(acetylamino)-3-carboxypropyl](hydroxy)phosphoryl]methyl}-6-aminoheptanedioic acid


Mass: 396.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H25N2O9P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 13-18% PEG 3350, 0.015 mM Tris pH 8 and 0.4 M NaI

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9796 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.9→39.03 Å / Num. obs: 41021 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 24.89 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.099 / Χ2: 0.947 / Net I/σ(I): 15.24 / Num. measured all: 297447
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-1.950.7770.8342.5821579297829770.898100
1.95-20.8490.6813.121358289028900.732100
2-2.060.8920.5284.0320934284128400.568100
2.06-2.120.9420.4085.220262279227920.44100
2.12-2.190.9560.3326.2719697266226620.357100
2.19-2.270.9740.287.418669257325720.301100
2.27-2.360.9820.2189.1718622251625160.235100
2.36-2.450.9840.2029.8517839241124110.217100
2.45-2.560.9870.16511.7817213232723260.177100
2.56-2.690.9910.13813.9216148220222020.149100
2.69-2.830.9940.11316.2815726213021300.121100
2.83-30.9960.09119.5614759200420040.098100
3-3.210.9970.07324.2513798188818880.078100
3.21-3.470.9980.05729.7512800177517750.061100
3.47-3.80.9990.04733.9211639163816380.05100
3.8-4.250.9990.0438.4810423149314930.043100
4.25-4.910.9990.03741.089204132513250.04100
4.91-6.010.9990.0438.717873115211520.043100
6.01-8.50.9990.03938.9158738998990.042100
8.50.9990.03142.1930315375290.03498.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4WCK

4wck


Resolution: 1.9→39.028 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2194 2050 5 %
Rwork0.1805 38965 -
obs0.1824 41015 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.26 Å2 / Biso mean: 37.7862 Å2 / Biso min: 10.6 Å2
Refinement stepCycle: final / Resolution: 1.9→39.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 73 284 3750
Biso mean--29.22 38.1 -
Num. residues----420
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093516
X-RAY DIFFRACTIONf_angle_d1.2034754
X-RAY DIFFRACTIONf_chiral_restr0.051514
X-RAY DIFFRACTIONf_plane_restr0.006619
X-RAY DIFFRACTIONf_dihedral_angle_d14.251346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.94420.35131330.279525412674
1.9442-1.99280.2651340.24725472681
1.9928-2.04670.21831360.2225742710
2.0467-2.10690.23141350.214825642699
2.1069-2.17490.27811340.204225462680
2.1749-2.25270.22151350.200825612696
2.2527-2.34280.24881350.188925622697
2.3428-2.44950.23961370.183826042741
2.4495-2.57860.20671360.188225922728
2.5786-2.74010.24071360.186925792715
2.7401-2.95160.23741370.190725992736
2.9516-3.24850.24751370.176726032740
3.2485-3.71820.21411390.166426412780
3.7182-4.68330.17251390.138726572796
4.6833-39.03580.18781470.173727952942
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)
10.4915-0.0505-0.11920.019-0.05570.15480.1639-0.12830.26110.0263-0.14630.01180.0348-0.09870.05860.1697-0.01940.01410.1007-0.02780.25575.134540.60135.9651
20.86420.04670.28370.5749-0.29511.16040.13870.1020.0928-0.0757-0.0593-0.00730.1337-0.10940.07660.12420.00340.00770.11080.020.14672.492431.7214-5.9549
30.43960.06880.90430.2027-0.09981.05540.0273-0.26050.05420.00310.0591-0.11760.2202-0.42860.11150.1537-0.0766-0.01030.24150.00420.11614.310426.653620.1695
40.4270.05150.29670.30050.23231.15930.182-0.06710.07830.0648-0.0858-0.16540.0673-0.49420.00450.30450.0002-0.03250.424-0.04680.18156.551726.216442.6683
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 19 through 65 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 66 through 247 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 339 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 340 through 438 )A0

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