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- PDB-3mn8: Structure of Drosophila melanogaster carboxypeptidase D isoform 1... -

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Basic information

Entry
Database: PDB / ID: 3mn8
TitleStructure of Drosophila melanogaster carboxypeptidase D isoform 1B short
ComponentsLP15968p
KeywordsHYDROLASE / catalytic domain of alpha/beta-hydrolase fold / C-terminal / all-beta transthyretin-like domain
Function / homology
Function and homology information


metallocarboxypeptidase D / peptide metabolic process / metallocarboxypeptidase activity / zinc ion binding
Similarity search - Function
Peptidase M14B, caboxypeptidase D / Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain / Carboxypeptidase-like, regulatory domain superfamily / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases ...Peptidase M14B, caboxypeptidase D / Carboxypeptidase regulatory-like domain / Carboxypeptidase-like, regulatory domain / Carboxypeptidase-like, regulatory domain superfamily / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
(2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID / Carboxypeptidase D
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTanco, S. / Arolas, J.L. / Guevara, T. / Lorenzo, J. / Aviles, F.X. / Gomis-Ruth, F.X.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structure-Function Analysis of the Short Splicing Variant Carboxypeptidase Encoded by Drosophila melanogaster silver.
Authors: Tanco, S. / Arolas, J.L. / Guevara, T. / Lorenzo, J. / Aviles, F.X. / Gomis-Ruth, F.X.
History
DepositionApr 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Sep 6, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: LP15968p
B: LP15968p
C: LP15968p
D: LP15968p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,89720
Polymers194,4424
Non-polymers2,45616
Water3,801211
1
A: LP15968p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4097
Polymers48,6101
Non-polymers7986
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LP15968p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1324
Polymers48,6101
Non-polymers5223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: LP15968p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2245
Polymers48,6101
Non-polymers6144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: LP15968p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1324
Polymers48,6101
Non-polymers5223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.020, 135.700, 141.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 39:158 or resseq 163:180 or resseq 195:336 )
211chain B and (resseq 39:158 or resseq 163:180 or resseq 195:336 )
311chain C and (resseq 39:158 or resseq 163:180 or resseq 195:336 )
411chain D and (resseq 39:158 or resseq 163:180 or resseq 195:336 )
112chain A and (resseq 337:344 or resseq 350:403 or resseq 407:417 )
212chain B and (resseq 337:344 or resseq 350:403 or resseq 407:417 )
312chain C and (resseq 337:344 or resseq 350:403 or resseq 407:417 )
412chain D and (resseq 337:344 or resseq 350:403 or resseq 407:417 )

NCS ensembles :
ID
1
2

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
LP15968p / metallocarboxypeptidase


Mass: 48610.375 Da / Num. of mol.: 4 / Fragment: UNP residues 1-435
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: svr-RF / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: D3DME3
#2: 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.: 4
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 , 4 types, 223 molecules

#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-GEM / (2-GUANIDINOETHYLMERCAPTO)SUCCINIC ACID / 2-GUANIDINOETHYLTHIO)SUCCINIC ACID / GUANIDINOETHYL MERCAPTOSUCCINIC ACID / GEMSA


Mass: 235.261 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H13N3O4S
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.4 Å3/Da / Density % sol: 48.72 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8% PEG 4000, 0.2M KSCN, 0.1M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 2, 2009
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.7→49 Å / Num. obs: 52035

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Processing

Software
NameVersionClassification
ProDCdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8L

1h8l


Resolution: 2.7→49 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 1.35 / Phase error: 35.98 / Stereochemistry target values: TWIN_LSQ_F
Details: THE CURRENTLY DEPOSITED COORDINATES WERE SUBJECTED TO A VERY FINAL REFINEMENT STEP UNDER CONSIDERATION OF DIFFERENT TLS GROUPS. ACCORDINGLY, THERE ARE MINOR DIFFERENCES BETWEEN THE CURRENT ...Details: THE CURRENTLY DEPOSITED COORDINATES WERE SUBJECTED TO A VERY FINAL REFINEMENT STEP UNDER CONSIDERATION OF DIFFERENT TLS GROUPS. ACCORDINGLY, THERE ARE MINOR DIFFERENCES BETWEEN THE CURRENT STATISTICS AND THOSE REPORTED IN THE PRIMARY PUBLICATION, WHICH ARE NOT SIGNIFICANT.
RfactorNum. reflection% reflection
Rfree0.2817 765 1.47 %
Rwork0.2108 --
obs0.2116 52035 99.97 %
all-52035 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.132 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--13.9933 Å20 Å2-0 Å2
2--15.5254 Å2-0 Å2
3----4.0673 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12113 0 144 211 12468
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812561
X-RAY DIFFRACTIONf_angle_d1.11816995
X-RAY DIFFRACTIONf_dihedral_angle_d20.1714553
X-RAY DIFFRACTIONf_chiral_restr0.0711823
X-RAY DIFFRACTIONf_plane_restr0.0042267
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2203X-RAY DIFFRACTIONPOSITIONAL
12B2203X-RAY DIFFRACTIONPOSITIONAL0.133
13C2203X-RAY DIFFRACTIONPOSITIONAL0.134
14D2203X-RAY DIFFRACTIONPOSITIONAL0.115
21A570X-RAY DIFFRACTIONPOSITIONAL
22B570X-RAY DIFFRACTIONPOSITIONAL0.16
23C570X-RAY DIFFRACTIONPOSITIONAL0.139
24D570X-RAY DIFFRACTIONPOSITIONAL0.144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.90880.3341470.245410085X-RAY DIFFRACTION99
2.9088-3.20090.32081560.222110098X-RAY DIFFRACTION98
3.2009-3.66270.28811420.201710180X-RAY DIFFRACTION99
3.6627-4.60920.24331500.187910245X-RAY DIFFRACTION99
4.6092-24.01790.27821540.21710570X-RAY DIFFRACTION99
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)
12.4003-0.6114-0.72531.41280.67242.04970.13970.60220.1664-0.2141-0.0229-0.1788-0.1993-0.0942-00.1690.03190.02010.11710.01510.145913.7723-13.5882-21.7594
20.5235-0.1814-0.22250.11390.09710.1243-0.1150.01030-0.0728-0.0656-0.0732-0.05980.0379-0.00360.47350.04380.04550.57160.0760.20683.4188-14.7408-29.1434
31.0465-0.57360.48570.91740.29821.5099-0.0034-0.21540.17940.13160.02860.16160.0224-0.2275-00.1740.01540.0467-0.0345-0.03480.24372.8757-7.16332.5295
41.8663-0.07890.06461.365-0.27281.4155-0.04670.2216-0.25040.00350.09570.31610.1017-0.22550.00010.07970.0110.03020.10920.00410.168115.1905-46.2737-0.7561
50.7249-0.3646-0.04870.79990.38070.8674-0.0918-0.4030.25430.22140.1042-0.0919-0.18640.02550.00030.28460.07130.01670.1788-0.02010.160621.7399-26.013316.7833
60.25280.04540.18670.0430.02290.2311-0.0012-0.0232-0.1307-0.0537-0.0340.10840.03670.01620.00010.3133-0.02790.08630.2116-0.1480.356826.3924-51.3109-3.6543
71.47530.04040.17131.2373-0.23952.51070.0484-0.3929-0.0761-0.0214-0.0126-0.02070.27580.061300.10130.0164-0.01660.12770.05410.0676-7.86922.77926.8777
80.7328-0.14660.38260.9176-0.45240.613-0.0169-0.64350.4276-0.0448-0.0308-0.266-0.26780.23940.00050.2293-0.05720.03080.372-0.08940.27221.963947.944923.0751
90.74120.43110.24240.39540.23430.14250.1017-0.1037-0.031-0.00310.13140.1166-0.04320.10440.0020.4448-0.0480.07480.3250.10820.60152.350915.980329.1542
101.97640.1492-0.27831.3720.17632.1297-0.06410.3792-0.0536-0.10540.0396-0.00640.01930.266900.10130.0459-0.01460.19030.0380.1018-9.48527.6366-11.612
110.72440.05210.72420.88720.25030.76880.069-0.00990.43750.0425-0.0390.4364-0.34-0.2378-0.00030.34670.06570.04720.13440.0530.4642-16.707951.8684-0.1554
120.01440.0292-0.01650.0592-0.03340.01880.06640.11850.0227-0.06960.1540.07410.04310.01720.00260.2846-0.05030.00820.46920.15620.3074-21.004422.8362-14.9256
130.1419-0.1642-0.05170.25860.0607-0.0038-0.0207-0.04140.00490.02180.04130.0692-0.01110.0702-00.1497-0.02870.03950.2118-0.01130.16421.72231.20150.0132
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 29:182 or resid 191:336
2X-RAY DIFFRACTION2chain A and resid 601
3X-RAY DIFFRACTION3chain A and resid 337:419
4X-RAY DIFFRACTION4chain B and (resid 28:184 or resid 192:336
5X-RAY DIFFRACTION5chain B and resid 337:420
6X-RAY DIFFRACTION6chain B and resid 601
7X-RAY DIFFRACTION7chain C and (resid 30:183 or resid 189:336
8X-RAY DIFFRACTION8chain C and resid 337:419
9X-RAY DIFFRACTION9chain C and resid 601
10X-RAY DIFFRACTION10chain D and (resid 27:181 or resid 191:336
11X-RAY DIFFRACTION11chain D and resid 337:420
12X-RAY DIFFRACTION12chain D and resid 601
13X-RAY DIFFRACTION13(chain A and resid 1001:1050) or (chain B and resid 1001:1054) or (chain C and resid 1001:1051) or (chain D and resid 1001:1056)

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