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- PDB-4b6z: Crystal structure of metallo-carboxypeptidase from Burkholderia c... -

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Basic information

Entry
Database: PDB / ID: 4b6z
TitleCrystal structure of metallo-carboxypeptidase from Burkholderia cenocepacia
ComponentsFAMILY M14 UNASSIGNED PEPTIDASE
KeywordsHYDROLASE
Function / homology
Function and homology information


metallocarboxypeptidase activity / proteolysis / zinc ion binding
Similarity search - Function
Immunoglobulin-like - #3120 / Cytosolic carboxypeptidase, N-terminal / : / Cytosolic carboxypeptidase N-terminal domain / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase ...Immunoglobulin-like - #3120 / Cytosolic carboxypeptidase, N-terminal / : / Cytosolic carboxypeptidase N-terminal domain / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / Family M14 unassigned peptidase
Similarity search - Component
Biological speciesBURKHOLDERIA CENOCEPACIA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRimsa, V. / Eadsforth, T.C. / Joosten, R.P. / Hunter, W.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: High-Resolution Structure of the M14-Type Cytosolic Carboxypeptidase from Burkholderia Cenocepacia Refined Exploiting Pdb_Redo Strategies.
Authors: Rimsa, V. / Eadsforth, T.C. / Joosten, R.P. / Hunter, W.N.
History
DepositionAug 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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: FAMILY M14 UNASSIGNED PEPTIDASE
B: FAMILY M14 UNASSIGNED PEPTIDASE
C: FAMILY M14 UNASSIGNED PEPTIDASE
D: FAMILY M14 UNASSIGNED PEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,75932
Polymers180,7864
Non-polymers1,97428
Water18,8981049
1
A: FAMILY M14 UNASSIGNED PEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5976
Polymers45,1961
Non-polymers4015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FAMILY M14 UNASSIGNED PEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6658
Polymers45,1961
Non-polymers4687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: FAMILY M14 UNASSIGNED PEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,6358
Polymers45,1961
Non-polymers4387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FAMILY M14 UNASSIGNED PEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,86310
Polymers45,1961
Non-polymers6669
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.897, 85.947, 289.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
FAMILY M14 UNASSIGNED PEPTIDASE


Mass: 45196.402 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ZINC IS COORDINATED BY H171, E174, H268 / Source: (gene. exp.) BURKHOLDERIA CENOCEPACIA (bacteria) / Strain: J2315 / LMG 16656 / Plasmid: PET15BTEV / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: B4EEQ5

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Non-polymers , 7 types, 1077 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1049 / 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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growDetails: 100 NL OF PROTEIN SOLUTION (10 MG ML-1 IN 100 MM SODIUM ACETATE PH 5.0, 150 MM NACL AND 0.5 MM ZINC SULPHATE) WERE MIXED AT 1:1 RATIO WITH RESERVOIR (0.2M LITHIUM SULPHATE, 25% PEG 3350 AND ...Details: 100 NL OF PROTEIN SOLUTION (10 MG ML-1 IN 100 MM SODIUM ACETATE PH 5.0, 150 MM NACL AND 0.5 MM ZINC SULPHATE) WERE MIXED AT 1:1 RATIO WITH RESERVOIR (0.2M LITHIUM SULPHATE, 25% PEG 3350 AND 0.1M BIS-TRIS, PH 5.5) EQUILIBRATED AGAINST A 70 UL RESERVOIR. CRYSTALS WERE OBSERVED AFTER THREE DAYS.

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 17, 2011 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. obs: 124234 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.4
Reflection shellResolution: 1.9→2 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3K2K

3k2k


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.009 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. RESIDUE 1 IN CHAINS A,B AND C. RESIDUES 157-158 IN CHAINS A,C. RESIDUE 319 IN CHAIN B, RESIDUES 315- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES ARE DISORDERED. RESIDUE 1 IN CHAINS A,B AND C. RESIDUES 157-158 IN CHAINS A,C. RESIDUE 319 IN CHAIN B, RESIDUES 315-319 IN CHAIN C, RESIDUES 316-319 IN CHAIN D. RESIDUES 384 IN CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.20455 6246 5 %RANDOM
Rwork0.16439 ---
obs0.16641 117888 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.436 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2--1.11 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11931 0 112 1049 13092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212786
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1431.94317411
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80151615
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.89723.516640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.856151986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.011599
X-RAY DIFFRACTIONr_chiral_restr0.080.21813
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110146
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 434 -
Rwork0.241 8081 -
obs--99.96 %
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)
11.46720.0179-0.05130.72380.01291.1509-0.0010.02040.1059-0.07320.01060.0524-0.0767-0.1089-0.00960.07020.0261-0.01240.06990.01620.064.21480.4475-50.9993
20.8539-0.00260.21071.08090.18060.77330.02090.0444-0.0649-0.01150.0363-0.1450.05870.0605-0.05720.07080.00410.00670.0672-0.00290.063227.3249-15.3644-54.2709
31.04370.13820.12071.05180.21650.81640.01740.2676-0.0532-0.22590.0419-0.0801-0.0290.0655-0.05930.12660.00670.00640.13570.00680.050922.6293-14.1199-68.8499
40.80960.0135-0.03310.2438-0.03650.48020.01940.01210.03360.00930.002-0.0015-0.01190.0185-0.02140.05870.0026-0.00220.045-0.00370.047723.6535-6.1846-28.7347
51.0451-0.0165-0.07080.9163-0.42080.88460.0313-0.22870.12660.20640.00150.0431-0.14880.0001-0.03280.1088-0.01410.01250.0962-0.03980.062116.80480.8447-12.6177
68.7606-0.1446-4.80571.21470.60134.1818-0.0364-0.1884-0.20190.0845-0.03540.03450.0575-0.0550.07190.0784-0.0002-0.02530.04770.01710.03815.6951-14.3135-14.999
71.15220.12280.27640.97870.14741.10580.0224-0.0491-0.1032-0.0320.0198-0.07970.0760.0292-0.04210.05320.00370.00180.03920.00370.069626.407829.0735-37.1705
80.7599-0.0708-0.01070.6568-0.21620.7938-0.00840.1096-0.06-0.13570.01860.11570.0236-0.0775-0.01020.0853-0.0114-0.040.0701-0.01830.07525.722338.3337-54.7024
90.7193-0.09470.28780.8315-0.52020.9163-0.03430.2425-0.0564-0.19840.00580.01780.0560.06590.02840.1187-0.0074-0.00890.1091-0.02310.067815.233638.7493-61.3601
101.0287-0.1517-0.00210.98970.03361.41180.02860.0663-0.0530.0127-0.05910.16760.0151-0.18360.03050.0242-0.0173-0.00410.1185-0.02030.1196-10.571140.9249-28.3923
110.53150.0377-0.06690.43170.24160.77340.0038-0.0405-0.0180.06380.0086-0.01260.02820.0334-0.01240.052-0.0016-0.0010.0530.00450.051913.432744.4023-12.703
120.8496-0.2990.39770.71590.02581.113-0.0398-0.1511-0.00770.10570.04330.09420.0158-0.0663-0.00350.07130.00620.02390.0740.00380.0775.918249.6338-7.3168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 110
2X-RAY DIFFRACTION2A111 - 235
3X-RAY DIFFRACTION3A236 - 383
4X-RAY DIFFRACTION4B2 - 226
5X-RAY DIFFRACTION5B227 - 355
6X-RAY DIFFRACTION6B356 - 384
7X-RAY DIFFRACTION7C2 - 110
8X-RAY DIFFRACTION8C111 - 301
9X-RAY DIFFRACTION9C302 - 384
10X-RAY DIFFRACTION10D1 - 110
11X-RAY DIFFRACTION11D111 - 308
12X-RAY DIFFRACTION12D309 - 384

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