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- PDB-3fx6: X-RAY crystallographic studies on the complex of carboxypeptidase... -

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Basic information

Entry
Database: PDB / ID: 3fx6
TitleX-RAY crystallographic studies on the complex of carboxypeptidase A with the inhibitor using alpha-nitro ketone as the zinc-binding group
ComponentsCarboxypeptidase A1
KeywordsHYDROLASE / alpha-nitro ketone / inhibitor / Carboxypeptidase / Metal-binding / Metalloprotease / Polymorphism / Protease / Secreted / Zinc / Zymogen
Function / homology
Function and homology information


carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase A, 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. / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase ...Carboxypeptidase A, 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. / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BPX / Carboxypeptidase A1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.851 Å
AuthorsWang, S.F. / Jin, J.Y. / Tian, G.R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Characterization of alpha-nitromethyl ketone as a new zinc-binding group based on structural analysis of its complex with carboxypeptidase A
Authors: Wang, S.F. / Tian, G.R. / Zhang, W.Z. / Jin, J.Y.
History
DepositionJan 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxypeptidase A1
C: Carboxypeptidase A1
E: Carboxypeptidase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5149
Polymers103,5103
Non-polymers1,0046
Water9,800544
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Carboxypeptidase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8383
Polymers34,5031
Non-polymers3352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Carboxypeptidase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8383
Polymers34,5031
Non-polymers3352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: Carboxypeptidase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8383
Polymers34,5031
Non-polymers3352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.356, 59.752, 99.514
Angle α, β, γ (deg.)90.00, 104.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carboxypeptidase A1


Mass: 34503.453 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: Bovine pancreas / References: UniProt: P00730, carboxypeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BPX / (2R)-4,4-dihydroxy-5-nitro-2-(phenylmethyl)pentanoic acid


Mass: 269.251 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H15NO6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 7.5
Details: 0.15M lithium chloride, 0.02% glutaraldehyde, 0.025M Tris, pH7.5, MICRODIALYSIS, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 27, 2008 / Details: oscillation
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→36.37 Å / Num. all: 67762 / Num. obs: 67762 / % possible obs: 89.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 49.1156
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Mean I/σ(I) obs: 30.398 / Rsym value: 0.081 / % possible all: 87.7

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
HKL-2000data reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HDQ

1hdq


Resolution: 1.851→36.37 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3261 5.1 %RANDOM
Rwork0.207 ---
obs0.207 60986 89.9 %-
all-71486 --
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 15.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.56 Å2
2---0.76 Å20 Å2
3---0.29 Å2
Refine analyzeLuzzati coordinate error free: 0.182 Å
Refinement stepCycle: LAST / Resolution: 1.851→36.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 60 544 7924
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.22
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.851→1.899 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 238 5.1 %
Rwork0.23 4504 -
obs-60987 90.27 %

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