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- PDB-2bo9: Human carboxypeptidase A4 in complex with human latexin. -

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Basic information

Entry
Database: PDB / ID: 2bo9
TitleHuman carboxypeptidase A4 in complex with human latexin.
Components
  • CARBOXYPEPTIDASE A4
  • HUMAN LATEXIN
KeywordsHYDROLASE / METALLOCARBOXYPEPTIDASE / X-RAY CRYSTAL STRUCTURE / ENDOGENOUS PROTEIN INHIBITOR / LATEXIN / METALLOPROTEASE CARBOXYPEPTIDASE
Function / homology
Function and homology information


metalloendopeptidase inhibitor activity / hormone catabolic process / peptide catabolic process / detection of temperature stimulus involved in sensory perception of pain / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / heparin binding / inflammatory response / proteolysis / extracellular space ...metalloendopeptidase inhibitor activity / hormone catabolic process / peptide catabolic process / detection of temperature stimulus involved in sensory perception of pain / Hydrolases; Acting on peptide bonds (peptidases); Metallocarboxypeptidases / metallocarboxypeptidase activity / heparin binding / inflammatory response / proteolysis / extracellular space / zinc ion binding / cytoplasm
Similarity search - Function
Proteinase inhibitor I47, latexin / Latexin N-terminal / Carboxypeptidase A, carboxypeptidase domain / Nuclear Transport Factor 2; Chain: A, - #10 / 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. ...Proteinase inhibitor I47, latexin / Latexin N-terminal / Carboxypeptidase A, carboxypeptidase domain / Nuclear Transport Factor 2; Chain: A, - #10 / 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 / Nuclear Transport Factor 2; Chain: A, / Aminopeptidase / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETONE / VALINE / Latexin / Carboxypeptidase A4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsPallares, I. / Bonet, R. / Garcia-Castellanos, R. / Ventura, S. / Aviles, F.X. / Vendrell, J. / Gomis-Rueth, F.X.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of Human Carboxypeptidase A4 with its Endogenous Protein Inhibitor, Latexin.
Authors: Pallares, I. / Bonet, R. / Garcia-Castellanos, R. / Ventura, S. / Aviles, F.X. / Vendrell, J. / Gomis-Rueth, F.X.
History
DepositionApr 8, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionApr 15, 2005ID: 2BK7
Revision 1.0Apr 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A4
B: HUMAN LATEXIN
C: CARBOXYPEPTIDASE A4
D: HUMAN LATEXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,00723
Polymers120,7244
Non-polymers2,28419
Water20,7711153
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.922, 96.651, 92.358
Angle α, β, γ (deg.)90.00, 99.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein CARBOXYPEPTIDASE A4 / CARBOXYPEPTIDASE A3 / UNQ694/PRO1339


Mass: 34564.723 Da / Num. of mol.: 2 / Fragment: ALPHA/BETA-HYDROLASE DOMAIN, RESIDUES 114-421
Source method: isolated from a genetically manipulated source
Details: N-GLYCOSYLATION AT ASN148 IN BOTH COPIES PRESENT. / Source: (gene. exp.) HOMO SAPIENS (human)
Description: CDNA PROVIDED BY DRS.HUANG AND SMITH, MAYO CLINIC, ROCHESTER, MN.
Plasmid: PPIC9 / Production host: PICHIA PASTORIS (fungus) / References: UniProt: Q9UI42
#2: Protein HUMAN LATEXIN / MUM


Mass: 25797.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGAT2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BS40

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Sugars , 1 types, 2 molecules

#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1170 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-ACN / ACETONE


Mass: 58.079 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1153 / 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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 6.5 / Details: 40% MPD; 0.1M BIS-TRIS PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0067
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0067 Å / Relative weight: 1
ReflectionResolution: 1.6→48.3 Å / Num. obs: 179401 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.8 / % possible all: 99.3

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Processing

Software
NameVersionClassification
DMmodel building
SCALAdata scaling
AMoREphasing
MLPHAREphasing
SIGMAAphasing
DMphasing
REFMAC5.1.9999refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CPA4 WITHIN PCPA4

Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.467 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS NCS BETWEEN THE COMPLEX FORMED BY MOLECULES A-C AND COMPLEX B-D. IN MOLECULES B AND D, RESIDUES 218-222 ARE DISORDERED. THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE IS NCS BETWEEN THE COMPLEX FORMED BY MOLECULES A-C AND COMPLEX B-D. IN MOLECULES B AND D, RESIDUES 218-222 ARE DISORDERED. THE COORDINATES OF HUMAN PROCARBOXYPEPTIDASE A4 EMPLOYED FOR THE MR CORRESPOND TO PDB ENTRY 2BOA.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 678 0.4 %RANDOM
Rwork0.149 ---
obs0.15 178706 99.8 %-
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: 17.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.98 Å20 Å2-0.24 Å2
2---1.36 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8404 0 146 1153 9703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228811
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3481.93311984
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18751044
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36124.421432
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03151440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3681547
X-RAY DIFFRACTIONr_chiral_restr0.0970.21281
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026737
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2070.24224
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2974
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8841.55399
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34328532
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.12633931
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3574.53452
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.19 58
Rwork0.17 13087
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)
10.2499-0.1001-0.11010.56230.05610.5673-0.00140.0163-0.0001-0.00750.0094-0.01210.0169-0.0057-0.008-0.0666-0.0013-0.0001-0.0524-0.0012-0.03822.615943.902984.9449
20.3371-0.084-0.14510.65070.06770.6407-0.00120.0168-0.0023-0.01990.0033-0.01370.0225-0.0036-0.0021-0.06360.0001-0.0004-0.04880.0001-0.036722.619743.591385.0723
31.18890.08950.16930.5016-0.0230.9643-0.0125-0.07750.08230.0057-0.0350.1493-0.0698-0.21540.0475-0.09750.02820.0054-0.0001-0.0331-0.0041-4.045657.759594.428
41.3526-0.0020.07550.7436-0.011.22460.0068-0.08160.07410.0075-0.03890.1709-0.0799-0.26660.032-0.09890.02950.00440.0188-0.03240.0021-4.284557.624394.8258
50.2262-0.0962-0.02990.4082-0.10540.83480.01010.02860.0029-0.03340.0040.00340.00210.0311-0.0142-0.02580.0023-0.0018-0.05490.0004-0.045635.06648.115440.2271
60.2823-0.05010.02720.4756-0.10570.92530.00670.0330.0067-0.05080.00270.00470.00710.0341-0.0094-0.02220.0033-0.0004-0.05040.0003-0.040935.011848.430940.336
71.4221-0.03810.24380.37170.42241.59270.0747-0.0328-0.0434-0.0633-0.0103-0.15540.16560.2753-0.0644-0.0330.0526-0.0024-0.01160.0204-0.024157.151634.553858.2159
81.15730.01670.3440.67380.29351.78430.0413-0.0386-0.0385-0.05350.0096-0.19050.17570.3696-0.0509-0.06440.0540.00090.0470.0073-0.001357.204334.635458.6877
90.0502-0.0644-0.45421.09712.01956.14650.050.0325-0.0906-0.2135-0.0639-0.0268-0.335-0.12140.01390-0.00020.0001-0.00010029.527245.993658.9538
100.1953-0.0202-0.17690.16730.0190.6996-0.0034-0.00080.0007-0.0238-0.0010.00940.01660.01310.00440.0012-0.0009-0.01280.0031-0.00550.046527.569445.661668.577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 308
2X-RAY DIFFRACTION2A3 - 308
3X-RAY DIFFRACTION2A999
4X-RAY DIFFRACTION3B1 - 217
5X-RAY DIFFRACTION4B1 - 217
6X-RAY DIFFRACTION5C3 - 308
7X-RAY DIFFRACTION6C3 - 308
8X-RAY DIFFRACTION6C999
9X-RAY DIFFRACTION7D1 - 217
10X-RAY DIFFRACTION8D1 - 217
11X-RAY DIFFRACTION9A901
12X-RAY DIFFRACTION9A998
13X-RAY DIFFRACTION9C901
14X-RAY DIFFRACTION9C998
15X-RAY DIFFRACTION10L1 - 13
16X-RAY DIFFRACTION10W1 - 1153

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