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- PDB-1zg9: Crystal Structure of 5-{[amino(imino)methyl]amino}-2-(sulfanylmet... -

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Basic information

Entry
Database: PDB / ID: 1zg9
TitleCrystal Structure of 5-{[amino(imino)methyl]amino}-2-(sulfanylmethyl)pentanoic acid Bound to Activated Porcine Pancreatic Carboxypeptidase B
Componentsprocarboxypeptidase B
KeywordsHYDROLASE / CARBOXYPEPTIDASE B / EXOPEPTIDASE / THIOL BASED INHIBITOR
Function / homology
Function and homology information


carboxypeptidase B / metallocarboxypeptidase activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase B, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase ...Carboxypeptidase B, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-L06 / Carboxypeptidase B
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAdler, M. / Bryant, J. / Buckman, B. / Islam, I. / Larsen, B. / Finster, S. / Kent, L. / May, K. / Mohan, R. / Yuan, S. / Whitlow, M.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal structures of potent thiol-based inhibitors bound to carboxypeptidase b.
Authors: Adler, M. / Bryant, J. / Buckman, B. / Islam, I. / Larsen, B. / Finster, S. / Kent, L. / May, K. / Mohan, R. / Yuan, S. / Whitlow, M.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: procarboxypeptidase B
B: procarboxypeptidase B
C: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0329
Polymers104,2203
Non-polymers8126
Water8,431468
1
A: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0113
Polymers34,7401
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0113
Polymers34,7401
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0113
Polymers34,7401
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.839, 102.484, 136.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer that can be generated from either chain A, chain B, or chain C.

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Components

#1: Protein procarboxypeptidase B


Mass: 34739.859 Da / Num. of mol.: 3 / Fragment: Catalytic Domain / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P09955, carboxypeptidase B
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-L06 / 5-{[AMINO(IMINO)METHYL]AMINO}-2-(SULFANYLMETHYL)PENTANOIC ACID


Mass: 205.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H15N3O2S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 468 / 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: 2.2 Å3/Da / Density % sol: 44.5 %
Description: SOLVENT RING AT 2.23 (A) PREVENTED PROPER INTEGRATION OF PEAKS BETWEEN 2.29 AND 2.20 (A). REFLECTIONS IN THIS RANGE WERE DELETED FROM THE DATA SET. THE ORIGINAL DATA SET WAS 96.8%
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium chloride, Tris, sodium cacodylate, PEG 8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2000
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.081
21.081
ReflectionResolution: 2→20 Å / Num. obs: 58319 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 24.3 Å2 / Rsym value: 0.08 / Net I/σ(I): 6.7
Reflection shellResolution: 2→2.09 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3 / Num. unique all: 7551 / Rsym value: 0.25 / % possible all: 98.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
X-PLOR3.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAS CATALYTIC DOMAIN

1nas


Resolution: 2→8 Å / Isotropic thermal model: OVERALL / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 2246 3.8 %RANDOM
Rwork0.203 ---
all0.207 57345 --
obs0.206 56660 90.2 %-
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.6383 Å20 Å20 Å2
2---5.8171 Å20 Å2
3---6.4554 Å2
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 42 468 7830
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg1.828
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.44
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2-2.090.31532883.80.2757551755198.8
2.09-2.20.30862800.26247619100
2.2-2.29000
2.29-2.330.3155890.3116255699.9
2.33-2.510.27633070.23067682100
2.51-2.750.28223180.218771099.9
2.75-3.130.27433130.2023777399.8
3.13-3.860.28312970.1865781299.3
3.86-80.24063540.1612795799.3

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