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- PDB-3ly0: Crystal structure of metallo peptidase from Rhodobacter sphaeroid... -

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Basic information

Entry
Database: PDB / ID: 3ly0
TitleCrystal structure of metallo peptidase from Rhodobacter sphaeroides liganded with phosphinate mimic of dipeptide L-Ala-D-Ala
ComponentsDipeptidase AC. Metallo peptidase. MEROPS family M19
KeywordsHYDROLASE / Structural genomics / NYSGRC / target 9523c / metallo peptidase / phosphinate inhibitor / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


membrane dipeptidase / metallodipeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M19 / Membrane dipeptidase (Peptidase family M19) / Renal dipeptidase family profile. / Metal-dependent hydrolases / Metal-dependent hydrolase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-LY0 / Dipeptidase AC
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.399 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of metallo peptidase from Rhodobacter sphaeroides liganded with phosphinate mimic of dipeptide L-Ala-D-Ala
Authors: Fedorov, A.A. / Fedorov, E.V. / Cummings, J. / Raushel, F.M. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_auth_seq_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.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_seq_id / _struct_conn.ptnr2_label_asym_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 1.3Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Dipeptidase AC. Metallo peptidase. MEROPS family M19
B: Dipeptidase AC. Metallo peptidase. MEROPS family M19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,9858
Polymers80,3332
Non-polymers6526
Water11,494638
1
A: Dipeptidase AC. Metallo peptidase. MEROPS family M19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4934
Polymers40,1671
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dipeptidase AC. Metallo peptidase. MEROPS family M19
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4934
Polymers40,1671
Non-polymers3263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.649, 50.325, 81.436
Angle α, β, γ (deg.)83.65, 73.64, 67.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Dipeptidase AC. Metallo peptidase. MEROPS family M19


Mass: 40166.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: RHOS4_24130, RSP_0802 / Production host: Escherichia coli (E. coli) / References: UniProt: Q3IZQ3
#2: Chemical ChemComp-LY0 / (2R)-3-[(R)-[(1R)-1-aminoethyl](hydroxy)phosphoryl]-2-methylpropanoic acid


Mass: 195.153 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14NO4P
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.11 Å3/Da / Density % sol: 41.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG3350, 0.1M Tric-HCl, 0.2M magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.4→38.9 Å / Num. all: 123178 / Num. obs: 123178 / % possible obs: 95.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
PHENIX(phenix.refine: 1.5_2)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FDG

3fdg


Resolution: 1.399→33.129 Å / SU ML: 0.17 / σ(F): 2 / Phase error: 17.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 6191 5.03 %
Rwork0.1693 --
obs0.1704 123178 95.02 %
all-123178 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.144 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9267 Å2-1.4824 Å2-1.1529 Å2
2--2.1484 Å22.3402 Å2
3----3.0751 Å2
Refinement stepCycle: LAST / Resolution: 1.399→33.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5440 0 28 638 6106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065604
X-RAY DIFFRACTIONf_angle_d1.1127599
X-RAY DIFFRACTIONf_dihedral_angle_d16.3622075
X-RAY DIFFRACTIONf_chiral_restr0.076808
X-RAY DIFFRACTIONf_plane_restr0.0051013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3995-1.41540.27261790.26173710X-RAY DIFFRACTION89
1.4154-1.4320.2762090.24893768X-RAY DIFFRACTION93
1.432-1.44950.24891890.23673860X-RAY DIFFRACTION94
1.4495-1.46780.23752300.22193833X-RAY DIFFRACTION94
1.4678-1.48710.22621780.20993877X-RAY DIFFRACTION94
1.4871-1.50750.22052320.19713876X-RAY DIFFRACTION94
1.5075-1.52910.19782170.18493825X-RAY DIFFRACTION94
1.5291-1.55190.19032000.18353889X-RAY DIFFRACTION95
1.5519-1.57610.19832000.17073902X-RAY DIFFRACTION94
1.5761-1.6020.20352420.17423855X-RAY DIFFRACTION95
1.602-1.62960.19662190.16313896X-RAY DIFFRACTION95
1.6296-1.65920.19511940.15563918X-RAY DIFFRACTION95
1.6592-1.69110.19851960.15283925X-RAY DIFFRACTION96
1.6911-1.72570.18832240.15813954X-RAY DIFFRACTION96
1.7257-1.76320.18532010.15273861X-RAY DIFFRACTION96
1.7632-1.80420.18252190.15563964X-RAY DIFFRACTION96
1.8042-1.84930.1872120.14943929X-RAY DIFFRACTION96
1.8493-1.89930.18361970.15823935X-RAY DIFFRACTION96
1.8993-1.95520.1992000.15233970X-RAY DIFFRACTION97
1.9552-2.01830.17331980.15284005X-RAY DIFFRACTION96
2.0183-2.09040.17631990.15343997X-RAY DIFFRACTION97
2.0904-2.17410.17592000.15183949X-RAY DIFFRACTION97
2.1741-2.2730.1682110.15453983X-RAY DIFFRACTION96
2.273-2.39280.19451940.16193967X-RAY DIFFRACTION96
2.3928-2.54270.19612070.16683920X-RAY DIFFRACTION96
2.5427-2.73890.20152000.16763951X-RAY DIFFRACTION96
2.7389-3.01440.19472120.17673948X-RAY DIFFRACTION96
3.0144-3.45020.18412410.16243892X-RAY DIFFRACTION96
3.4502-4.34530.16812110.14653938X-RAY DIFFRACTION95
4.3453-33.1380.16851800.1693690X-RAY DIFFRACTION90

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