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

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Basic information

Entry
Database: PDB / ID: 4rzz
TitleCrystal structure of metallopeptidase-like dimethylsulphoniopropionate (DMSP) lyase RlDddP in complex with phosphate
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
: / PHOSPHATE ION / Peptidase M24
Similarity search - Component
Biological speciesSilicibacter lacuscaerulensis ITI-1157 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 27, 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)203,05120
Polymers201,8564
Non-polymers1,19516
Water35,1651952
1
A: Peptidase M24
C: Peptidase M24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,52610
Polymers100,9282
Non-polymers5988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9630 Å2
ΔGint-119 kcal/mol
Surface area27890 Å2
MethodPISA
2
B: Peptidase M24
D: Peptidase M24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,52610
Polymers100,9282
Non-polymers5988
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9710 Å2
ΔGint-117 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.610, 175.610, 109.574
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 ITI-1157 (bacteria)
Gene: SL1157_2466 / Production host: Escherichia coli (E. coli) / References: UniProt: D0CY07
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1952 / 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: 4.83 Å3/Da / Density % sol: 74.55 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M potassium/sodium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP

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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: 2.1→50 Å / Num. all: 201557 / Num. obs: 201557 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MLPHAREphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→38.02 Å / SU ML: 0.21 / σ(F): 0.05 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.194 10173 5.05 %
Rwork0.168 --
obs0.17 201557 91.6 %
all-201557 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.34 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.606 Å2-0 Å2-0 Å2
2--5.606 Å20 Å2
3----11.212 Å2
Refinement stepCycle: LAST / Resolution: 2.1→38.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13852 0 52 1952 15856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714220
X-RAY DIFFRACTIONf_angle_d1.03519284
X-RAY DIFFRACTIONf_dihedral_angle_d12.7925252
X-RAY DIFFRACTIONf_chiral_restr0.072048
X-RAY DIFFRACTIONf_plane_restr0.0042540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1022-2.1260.29782510.25025169X-RAY DIFFRACTION74
2.126-2.1510.27083210.25195759X-RAY DIFFRACTION83
2.151-2.17730.27973210.23535861X-RAY DIFFRACTION84
2.1773-2.20480.25953190.22885858X-RAY DIFFRACTION84
2.2048-2.23380.26393060.23185831X-RAY DIFFRACTION85
2.2338-2.26440.27642980.22426007X-RAY DIFFRACTION86
2.2644-2.29680.25023050.2065986X-RAY DIFFRACTION86
2.2968-2.33110.24093160.20256113X-RAY DIFFRACTION88
2.3311-2.36750.2032960.21046092X-RAY DIFFRACTION88
2.3675-2.40630.22883320.20656196X-RAY DIFFRACTION88
2.4063-2.44780.25493170.21226154X-RAY DIFFRACTION88
2.4478-2.49230.24993090.19646249X-RAY DIFFRACTION89
2.4923-2.54020.2263690.19536270X-RAY DIFFRACTION91
2.5402-2.5920.24093340.20386294X-RAY DIFFRACTION91
2.592-2.64840.23553390.19376375X-RAY DIFFRACTION91
2.6484-2.710.22143630.1886358X-RAY DIFFRACTION92
2.71-2.77770.20863700.18286509X-RAY DIFFRACTION93
2.7777-2.85280.23863400.18456507X-RAY DIFFRACTION94
2.8528-2.93670.21613360.18526635X-RAY DIFFRACTION95
2.9367-3.03150.21043770.18346673X-RAY DIFFRACTION96
3.0315-3.13980.19853720.17496722X-RAY DIFFRACTION96
3.1398-3.26540.19793940.16846675X-RAY DIFFRACTION97
3.2654-3.4140.18023590.16386794X-RAY DIFFRACTION98
3.414-3.59380.17883320.15996887X-RAY DIFFRACTION98
3.5938-3.81880.15173810.14166810X-RAY DIFFRACTION98
3.8188-4.11330.15233790.12616862X-RAY DIFFRACTION99
4.1133-4.52670.14433650.11486922X-RAY DIFFRACTION99
4.5267-5.18030.12563450.11216950X-RAY DIFFRACTION99
5.1803-6.52120.15053670.13256922X-RAY DIFFRACTION100
6.5212-38.02690.16433600.15476944X-RAY DIFFRACTION100

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