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- PDB-5hj1: Crystal structure of PDZ domain of pullulanase C protein of type ... -

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Basic information

Entry
Database: PDB / ID: 5hj1
TitleCrystal structure of PDZ domain of pullulanase C protein of type II secretion system from Klebsiella pneumoniae in complex with fatty acid
ComponentsPullulanase C protein
KeywordsHYDROLASE / GspC protein / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases
Function / homologyPDZ domain / Pdz3 Domain / Roll / Mainly Beta / VACCENIC ACID / :
Function and homology information
Biological speciesKlebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of PDZ domain of pullulanase C protein of type II secretion system from Klebsiella pneumoniae in complex with fatty acid
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 17, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pullulanase C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7122
Polymers11,4301
Non-polymers2821
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.636, 47.636, 93.202
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Pullulanase C protein


Mass: 11429.631 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 181-280)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044 (bacteria)
Gene: YP_002917874 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: A0A0M1T516
#2: Chemical ChemComp-VCA / VACCENIC ACID / (11E)-OCTADEC-11-ENOIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsThe ligand was identified based on the electron density maps and was not originally present in ...The ligand was identified based on the electron density maps and was not originally present in protein solution or crystallization conditions. Based on the results described by R. Mejia, et al., 1999 authors concluded that vaccenic acid is likely to bind to a protein.

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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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 4 M Formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 17852 / % possible obs: 99.6 % / Redundancy: 27.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 87.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 28.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
HKL-3000data scaling
HKL-3000phasing
REFMAC5.8.0135refinement
Cootmodel building
HKL-3000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.5→42.42 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.181 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The ligand was identified based on the electron density maps and was not originally present in protein solution or crystallization ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The ligand was identified based on the electron density maps and was not originally present in protein solution or crystallization conditions. Based on the results described by R. Mejia, et al., 1999 authors concluded that vaccenic acid is likely to bind to a protein.
RfactorNum. reflection% reflectionSelection details
Rfree0.22231 848 4.8 %RANDOM
Rwork0.192 ---
obs0.1934 16907 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0 Å2
2--0.23 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 20 78 857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019837
X-RAY DIFFRACTIONr_bond_other_d0.0010.02852
X-RAY DIFFRACTIONr_angle_refined_deg2.1562.0241129
X-RAY DIFFRACTIONr_angle_other_deg1.02931961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6045105
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.90424.7540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.89815145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.795158
X-RAY DIFFRACTIONr_chiral_restr0.130.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.021966
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02186
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2061.989411
X-RAY DIFFRACTIONr_mcbond_other2.1961.987410
X-RAY DIFFRACTIONr_mcangle_it3.3762.971519
X-RAY DIFFRACTIONr_mcangle_other3.3732.972520
X-RAY DIFFRACTIONr_scbond_it2.7992.539426
X-RAY DIFFRACTIONr_scbond_other2.7972.541427
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3753.627611
X-RAY DIFFRACTIONr_long_range_B_refined7.4219.808898
X-RAY DIFFRACTIONr_long_range_B_other7.4189.818899
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 58 -
Rwork0.204 1229 -
obs--99.61 %
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)
19.4067-4.1647-2.19654.4491-0.34771.25330.1475-0.2225-0.0074-0.1951-0.0973-0.0706-0.05180.1328-0.05030.1553-0.00290.07580.04560.04690.134917.737521.378629.7917
25.34380.0698-3.90160.55471.12737.5050.09460.07150.3301-0.104-0.02190.1516-0.2494-0.0976-0.07270.11510.0206-0.02560.02510.02970.11759.621527.891333.0124
32.6349-0.1916-0.9580.88130.21292.7533-0.03410.2398-0.03940.0118-0.0103-0.0114-0.0408-0.05190.04440.0065-0.0067-0.00070.0438-0.02190.049311.502412.390935.9484
47.8689-1.40691.93927.8646-1.22962.82560.03930.98750.5105-0.4034-0.1034-0.63710.2160.01720.06410.05120.02790.03630.2950.07620.102412.817914.010821.3478
50.5318-0.2043-0.76078.72716.23015.19990.10110.20350.17430.00220.1949-0.2099-0.1331-0.0785-0.2960.03960.0324-0.00450.11450.09050.14915.655923.592224.3739
66.417-3.49910.96123.9405-0.57022.4254-0.03260.4789-0.24010.0007-0.10050.18210.0049-0.11330.13310.0068-0.02090.00750.1089-0.02750.08242.918310.855733.9825
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A181 - 187
2X-RAY DIFFRACTION2A188 - 192
3X-RAY DIFFRACTION3A193 - 241
4X-RAY DIFFRACTION4A242 - 251
5X-RAY DIFFRACTION5A252 - 257
6X-RAY DIFFRACTION6A258 - 277

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