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- PDB-2g4v: anomalous substructure of proteinase K -

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Basic information

Entry
Database: PDB / ID: 2g4v
Titleanomalous substructure of proteinase K
ComponentsProteinase K
KeywordsHYDROLASE / anomalous substructure of proteinase K
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / : / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEngyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.14 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 6, 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 / diffrn_source / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE AUTHOR STATES THAT AMINO ACID 207 WAS MUTATED BY PERSUING ELECTRON DENSITY AT ATOMIC ...SEQUENCE AUTHOR STATES THAT AMINO ACID 207 WAS MUTATED BY PERSUING ELECTRON DENSITY AT ATOMIC RESOLUTION AND AFTER REPEATION OF MANY REFINEMENT CYCLE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1536
Polymers28,9591
Non-polymers1945
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.780, 67.780, 101.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-325-

HOH

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Components

#1: Protein Proteinase K / Tritirachium alkaline proteinase / Endopeptidase K


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.1 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.14→30 Å / Num. obs: 13684 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.14→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.938 / SU B: 8.999 / SU ML: 0.122 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20322 285 2.1 %RANDOM
Rwork0.1631 ---
obs0.16398 13399 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.808 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å20 Å2
2---0.51 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.14→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2031 0 5 130 2166
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0212072
X-RAY DIFFRACTIONr_angle_refined_deg1.7951.9362817
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20823.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.74615299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2451512
X-RAY DIFFRACTIONr_chiral_restr0.130.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021602
X-RAY DIFFRACTIONr_nbd_refined0.2190.21095
X-RAY DIFFRACTIONr_nbtor_refined0.3010.21401
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2870.2137
X-RAY DIFFRACTIONr_metal_ion_refined0.3480.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.219
X-RAY DIFFRACTIONr_mcbond_it1.0341.51370
X-RAY DIFFRACTIONr_mcangle_it1.6882.52176
X-RAY DIFFRACTIONr_scbond_it4.3995719
X-RAY DIFFRACTIONr_scangle_it6.06510641
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 16 -
Rwork0.196 968 -
obs--99.39 %
Refinement TLS params.Method: refined / Origin x: 16.1659 Å / Origin y: 12.972 Å / Origin z: 25.2282 Å
111213212223313233
T-0.0158 Å20.002 Å20.0002 Å2--0.0219 Å2-0.0015 Å2---0.0285 Å2
L0.8853 °20.032 °20.0254 °2-0.8167 °20.0203 °2--0.3498 °2
S-0.0058 Å °0.0105 Å °-0.0108 Å °0.0113 Å °-0.014 Å °-0.0348 Å °0.0115 Å °-0.0163 Å °0.0198 Å °

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