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- PDB-1cg2: CARBOXYPEPTIDASE G2 -

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Basic information

Entry
Database: PDB / ID: 1cg2
TitleCARBOXYPEPTIDASE G2
ComponentsCARBOXYPEPTIDASE G2Glutamate carboxypeptidase
KeywordsMETALLOCARBOXYPEPTIDASE / HYDROLASE
Function / homology
Function and homology information


glutamate carboxypeptidase / carboxypeptidase activity / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M20, glutamate carboxypeptidase / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 ...Peptidase M20, glutamate carboxypeptidase / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsRowsell, S. / Pauptit, R.A. / Tucker, A.D. / Melton, R.G. / Blow, D.M. / Brick, P.
Citation
Journal: Structure / Year: 1997
Title: Crystal structure of carboxypeptidase G2, a bacterial enzyme with applications in cancer therapy.
Authors: Rowsell, S. / Pauptit, R.A. / Tucker, A.D. / Melton, R.G. / Blow, D.M. / Brick, P.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: A New Crystal Form of Carboxypeptidase G2 from Pseudomonas Sp. Strain Rs-16 which is More Amenable to Structure Determination
Authors: Tucker, A.D. / Rowsell, S. / Melton, R.G. / Pauptit, R.A.
History
DepositionDec 20, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE G2
B: CARBOXYPEPTIDASE G2
C: CARBOXYPEPTIDASE G2
D: CARBOXYPEPTIDASE G2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,84417
Polymers166,9934
Non-polymers85013
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-543 kcal/mol
Surface area56560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.260, 105.280, 122.190
Angle α, β, γ (deg.)90.00, 109.54, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHERE ARE TWO MOLECULAR DIMERS CONTAINED WITHIN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT. THE FOUR SUBUNITS PACK TOGETHER WITH APPROXIMATE D2 SYMMETRY. THE SUBUNITS OF ONE MOLECULE HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *D*, WHILE THE SUBUNITS OF THE OTHER MOLECULE HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *B* AND *C*.

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Components

#1: Protein
CARBOXYPEPTIDASE G2 / Glutamate carboxypeptidase


Mass: 41748.359 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: RS-16 / Cell line: 293 / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P06621, glutamate carboxypeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEACH MONOMER CONSISTS OF TWO SEPARATE DOMAINS: A CATALYTIC DOMAIN CONTAINING RESIDUES 26 - 213, 326 ...EACH MONOMER CONSISTS OF TWO SEPARATE DOMAINS: A CATALYTIC DOMAIN CONTAINING RESIDUES 26 - 213, 326 - 414 AND A DIMERIZATION DOMAIN CONTAINING RESIDUES 214 - 325.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 12

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: HANGING DROPS WERE FORMED BY MIXING 4 MICROLITERS OF PROTEIN SOLUTION AT 16-20 MG/ML WITH 4 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 10-12% PEG 4000, 0.2M TRIS (PH 7.2), 0.2M ZINC ...Details: HANGING DROPS WERE FORMED BY MIXING 4 MICROLITERS OF PROTEIN SOLUTION AT 16-20 MG/ML WITH 4 MICROLITERS OF RESERVOIR SOLUTION CONTAINING 10-12% PEG 4000, 0.2M TRIS (PH 7.2), 0.2M ZINC ACETATE 10% GLYCEROL. CRYSTALS GREW AT 18-20 DEGREES WITHIN A FEW DAYS., vapor diffusion - hanging drop, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18-10 mg/mlenzyme1drop
25-6 %(w/v)PEG40001drop
3100 mMzinc acetate1drop
4100 mMTris-HCl1drop
55 %(v/v)glycerol1drop
610-12 %(w/v)PEG40001reservoir
7200 mMzinc acetate1reservoir
8200 mMTris-HCl1reservoir
910 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.92
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 18, 1996
RadiationMonochromator: Y / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 62936 / % possible obs: 93.9 % / Observed criterion σ(I): 0 / Redundancy: 3.57 % / Biso Wilson estimate: 41.2 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 6.41
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4 / % possible all: 90.4
Reflection
*PLUS
Num. measured all: 224872
Reflection shell
*PLUS
% possible obs: 90.4 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→20 Å / Rfactor Rfree error: 0.0045 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2461 3.66 %RANDOM
Rwork0.196 ---
obs0.196 62936 97.46 %-
Displacement parametersBiso mean: 37.5 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11122 0 13 331 11466
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.34
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.31
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.183
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 3 Å2 / Weight position: 100
LS refinement shellResolution: 2.5→2.61 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.301 277 3.31 %
Rwork0.196 7501 -
obs--89.57 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.31
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.183
LS refinement shell
*PLUS
Rfactor obs: 0.196

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