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- PDB-4rzy: Crystal structure of metallopeptidase-like dimethylsulphoniopropi... -

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Basic information

Entry
Database: PDB / ID: 4rzy
TitleCrystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with MES
ComponentsPeptidase M24
KeywordsLYASE / metallopeptidase-like DMSP lyase / DMSP lyase
Function / homology
Function and homology information


Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesSilicibacter lacuscaerulensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsZhang, Y. / Wang, P.
CitationJournal: Mol.Microbiol. / Year: 2015
Title: Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial Dimethylsulfoniopropionate lyase: a new enzyme from an old fold.
Authors: Wang, P. / Chen, X.L. / Li, C.Y. / Gao, X. / Zhu, D.Y. / Xie, B.B. / Qin, Q.L. / Zhang, X.Y. / Su, H.N. / Zhou, B.C. / Xun, L.Y. / Zhang, Y.Z.
History
DepositionDec 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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_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: Peptidase M24
B: Peptidase M24
C: Peptidase M24
D: Peptidase M24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,08416
Polymers201,8564
Non-polymers1,22812
Water41,6152310
1
A: Peptidase M24
C: Peptidase M24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5428
Polymers100,9282
Non-polymers6146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9440 Å2
ΔGint-85 kcal/mol
Surface area28100 Å2
MethodPISA
2
B: Peptidase M24
D: Peptidase M24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5428
Polymers100,9282
Non-polymers6146
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9460 Å2
ΔGint-86 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.301, 175.301, 109.689
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Peptidase M24


Mass: 50464.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Silicibacter lacuscaerulensis (bacteria)
Gene: SL1157_2466 / Production host: Escherichia coli (E. coli) / References: UniProt: D0CY07
#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2310 / 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: 2

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Sample preparation

CrystalDensity Matthews: 4.82 Å3/Da / Density % sol: 74.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 1 M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 1, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 272308 / Num. obs: 272308 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.02 Å / % possible all: 98.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.949→34.237 Å / SU ML: 0.17 / σ(F): 1.96 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 13754 5.05 %RANDOM
Rwork0.1629 ---
obs0.1642 272308 99.02 %-
all-272308 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.949→34.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13852 0 56 2310 16218
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714272
X-RAY DIFFRACTIONf_angle_d1.06819364
X-RAY DIFFRACTIONf_dihedral_angle_d13.5615300
X-RAY DIFFRACTIONf_chiral_restr0.0442052
X-RAY DIFFRACTIONf_plane_restr0.0052552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9494-1.97160.26114380.23568537X-RAY DIFFRACTION98
1.9716-1.99480.27384680.23178571X-RAY DIFFRACTION98
1.9948-2.01910.25534380.22118579X-RAY DIFFRACTION99
2.0191-2.04470.25724770.21948561X-RAY DIFFRACTION99
2.0447-2.07160.22594480.20638609X-RAY DIFFRACTION99
2.0716-2.09990.25884640.21028529X-RAY DIFFRACTION99
2.0999-2.12990.24824450.20428639X-RAY DIFFRACTION99
2.1299-2.16170.2214300.18788606X-RAY DIFFRACTION99
2.1617-2.19550.23584630.18858690X-RAY DIFFRACTION99
2.1955-2.23150.21464720.18578548X-RAY DIFFRACTION99
2.2315-2.270.23274730.19388584X-RAY DIFFRACTION99
2.27-2.31120.19734640.17438599X-RAY DIFFRACTION99
2.3112-2.35570.22254250.18098703X-RAY DIFFRACTION99
2.3557-2.40370.22084430.17568636X-RAY DIFFRACTION99
2.4037-2.4560.20584620.17878582X-RAY DIFFRACTION99
2.456-2.51310.19044710.17218617X-RAY DIFFRACTION99
2.5131-2.57590.21644580.17118655X-RAY DIFFRACTION99
2.5759-2.64560.18844430.16588730X-RAY DIFFRACTION99
2.6456-2.72340.20114800.16748568X-RAY DIFFRACTION99
2.7234-2.81120.19564810.1658586X-RAY DIFFRACTION99
2.8112-2.91170.19324740.16188680X-RAY DIFFRACTION100
2.9117-3.02820.19614410.16498675X-RAY DIFFRACTION99
3.0282-3.16590.19644780.15078586X-RAY DIFFRACTION99
3.1659-3.33270.15974600.14358684X-RAY DIFFRACTION99
3.3327-3.54130.16484480.148594X-RAY DIFFRACTION99
3.5413-3.81440.14554430.13418487X-RAY DIFFRACTION97
3.8144-4.19760.14274710.12048645X-RAY DIFFRACTION100
4.1976-4.80360.12454800.11738697X-RAY DIFFRACTION100
4.8036-6.04660.15264750.14248696X-RAY DIFFRACTION100
6.0466-34.24240.16624410.15988681X-RAY DIFFRACTION100

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