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- PDB-5giv: Crystal structure of M32 carboxypeptidase from Deinococcus radiod... -

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Basic information

Entry
Database: PDB / ID: 5giv
TitleCrystal structure of M32 carboxypeptidase from Deinococcus radiodurans R1
ComponentsCarboxypeptidase 1
KeywordsHYDROLASE / M32 carboxypeptidase / Cobalt / Metallopeptidase
Function / homology
Function and homology information


carboxypeptidase Taq / metallocarboxypeptidase activity / metal ion binding
Similarity search - Function
Peptidase M32, carboxypeptidase Taq / Carboxypeptidase Taq (M32) metallopeptidase / Neurolysin; domain 3 - #30 / Neurolysin; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Metal-dependent carboxypeptidase
Similarity search - Component
Biological speciesDeinococcus radiodurans str. R1 (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSharma, B. / Singh, R. / Yadav, P. / Ghosh, B. / Kumar, A. / Jamdar, S.N. / Makde, R.D.
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Active site gate of M32 carboxypeptidases illuminated by crystal structure and molecular dynamics simulations
Authors: Sharma, B. / Jamdar, S.N. / Ghosh, B. / Yadav, P. / Kumar, A. / Kundu, S. / Goyal, V.D. / Makde, R.D.
History
DepositionJun 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 8, 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
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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase 1
B: Carboxypeptidase 1
C: Carboxypeptidase 1
D: Carboxypeptidase 1
E: Carboxypeptidase 1
F: Carboxypeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,09713
Polymers337,6456
Non-polymers4517
Water16,340907
1
A: Carboxypeptidase 1
D: Carboxypeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,7385
Polymers112,5482
Non-polymers1903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-81 kcal/mol
Surface area38970 Å2
MethodPISA
2
B: Carboxypeptidase 1
F: Carboxypeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6794
Polymers112,5482
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-72 kcal/mol
Surface area39380 Å2
MethodPISA
3
C: Carboxypeptidase 1
E: Carboxypeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,6794
Polymers112,5482
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-72 kcal/mol
Surface area39100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.857, 256.632, 199.214
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Carboxypeptidase 1 /


Mass: 56274.246 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans str. R1 (radioresistant)
Strain: R1 / Gene: DR_2423 / Plasmid: pST50STR / Details (production host): pET3a, T7 based / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): pLysS / References: UniProt: Q9RRR3, carboxypeptidase Taq
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 907 / 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: 2.55 Å3/Da / Density % sol: 51.81 %
Crystal growTemperature: 294 K / Method: microbatch
Details: 100mM Sodium Cacodylate pH 6.5, 0.2M Mg acetate, 15% Glycerol, 20% Cymal, 20% PEG 8000
PH range: 6.5 to 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 22, 2014 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.4→47.97 Å / Num. obs: 134280 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.415 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.151 / Net I/σ(I): 14.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.608 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
Cootmodel building
PHASERphasing
Aimlessdata scaling
XDSdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HOA

3hoa


Resolution: 2.4→47.97 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2427 6738 5.03 %
Rwork0.2055 --
obs0.2074 134079 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23550 0 10 907 24467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00524153
X-RAY DIFFRACTIONf_angle_d0.66932784
X-RAY DIFFRACTIONf_dihedral_angle_d15.92914029
X-RAY DIFFRACTIONf_chiral_restr0.0413378
X-RAY DIFFRACTIONf_plane_restr0.0044395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.31532470.25464200X-RAY DIFFRACTION100
2.4273-2.45590.28652190.24754229X-RAY DIFFRACTION100
2.4559-2.48580.29682190.25014185X-RAY DIFFRACTION100
2.4858-2.51730.30832230.24814203X-RAY DIFFRACTION100
2.5173-2.55040.29612190.25394251X-RAY DIFFRACTION100
2.5504-2.58530.31982190.2574231X-RAY DIFFRACTION100
2.5853-2.62230.31192200.2494206X-RAY DIFFRACTION100
2.6223-2.66140.29472290.24784217X-RAY DIFFRACTION100
2.6614-2.7030.29642260.24514237X-RAY DIFFRACTION100
2.703-2.74730.28722150.25524207X-RAY DIFFRACTION100
2.7473-2.79470.31752230.24724253X-RAY DIFFRACTION100
2.7947-2.84550.27682400.24144189X-RAY DIFFRACTION100
2.8455-2.90020.26761980.24014263X-RAY DIFFRACTION100
2.9002-2.95940.2892370.23094208X-RAY DIFFRACTION100
2.9594-3.02370.27662050.2454234X-RAY DIFFRACTION100
3.0237-3.0940.27652120.24724231X-RAY DIFFRACTION100
3.094-3.17140.2882230.23424247X-RAY DIFFRACTION100
3.1714-3.25710.24582260.23414237X-RAY DIFFRACTION100
3.2571-3.3530.26992280.23084250X-RAY DIFFRACTION100
3.353-3.46120.2622430.21144248X-RAY DIFFRACTION100
3.4612-3.58480.24222040.20494244X-RAY DIFFRACTION100
3.5848-3.72830.22632200.19354276X-RAY DIFFRACTION100
3.7283-3.89790.20762220.17734239X-RAY DIFFRACTION100
3.8979-4.10330.20032290.17394273X-RAY DIFFRACTION100
4.1033-4.36020.20942040.16984287X-RAY DIFFRACTION100
4.3602-4.69660.18082410.15374263X-RAY DIFFRACTION100
4.6966-5.16880.19122380.16084291X-RAY DIFFRACTION100
5.1688-5.91550.23462350.17594274X-RAY DIFFRACTION100
5.9155-7.44840.20982230.17754342X-RAY DIFFRACTION99
7.4484-47.97910.15412510.14074326X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -46.9161 Å / Origin y: -35.0007 Å / Origin z: 41.2143 Å
111213212223313233
T0.2121 Å2-0.0038 Å2-0.0665 Å2-0.2396 Å2-0.0055 Å2--0.2452 Å2
L-0.0095 °2-0.0233 °2-0.0421 °2-0.0535 °20.0023 °2--0.0723 °2
S-0.0179 Å °0.0112 Å °0.0033 Å °-0.0265 Å °0.0191 Å °0.0507 Å °-0.0142 Å °-0.0116 Å °0.0029 Å °
Refinement TLS groupSelection details: ALL

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