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- PDB-3b2y: CRYSTAL STRUCTURE OF a putative metallopeptidase (SDEN_2526) FROM... -

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Basic information

Entry
Database: PDB / ID: 3b2y
TitleCRYSTAL STRUCTURE OF a putative metallopeptidase (SDEN_2526) FROM SHEWANELLA DENITRIFICANS OS217 AT 1.74 A RESOLUTION
ComponentsMetallopeptidase containing co-catalytic metalloactive site
KeywordsHYDROLASE / METALLOPEPTIDASE CONTAINING CO-CATALYTIC METALLOACTIVE SITE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
Succinylglutamate desuccinylase/aspartoacylase / Succinylglutamate desuccinylase / Aspartoacylase family / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / Uncharacterized protein
Similarity search - Component
Biological speciesShewanella denitrificans OS217 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.74 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of metallopeptidase containing co-catalytic metalloactive site (YP_563529.1) from Shewanella denitrificans OS217 at 1.74 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Metallopeptidase containing co-catalytic metalloactive site
B: Metallopeptidase containing co-catalytic metalloactive site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2774
Polymers61,1592
Non-polymers1172
Water4,143230
1
A: Metallopeptidase containing co-catalytic metalloactive site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6382
Polymers30,5801
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Metallopeptidase containing co-catalytic metalloactive site
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6382
Polymers30,5801
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.715, 127.577, 49.303
Angle α, β, γ (deg.)90.000, 116.280, 90.000
Int Tables number4
Space group name H-MP1211
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Metallopeptidase containing co-catalytic metalloactive site


Mass: 30579.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella denitrificans OS217 (bacteria)
Species: Shewanella denitrificans / Strain: OS217, DSM 15013 / Gene: YP_563529.1, Sden_2526 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q12L70
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsREMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE REMARK 999 LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. REMARK 999

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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: 2.02 Å3/Da / Density % sol: 38.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.07
Details: NANODROP, 20.4% PEG 6000, 0.1M MES pH 6.07, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9794, 1.0000, 0.9797
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2007 / Details: KOHZU, Double crystal Si(111)
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
211
30.97971
ReflectionResolution: 1.74→28.82 Å / Num. obs: 46761 / % possible obs: 94.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 28.085 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 7.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.74-1.791.70.382600034750.3895.4
1.79-1.831.90.3022.5663234870.30296.8
1.83-1.891.90.2531.2635633490.25397.5
1.89-1.951.90.2081.1616232280.20897
1.95-2.011.90.1264.2606131530.12696.4
2.01-2.081.90.1251.1583230560.12596.1
2.08-2.161.90.088.6559629030.0896.2
2.16-2.251.90.0735.9548128260.07396.1
2.25-2.351.90.0755.2514826570.07594.4
2.35-2.461.90.05710.5495725470.05795.5
2.46-2.5920.04813.2474424150.04894.4
2.59-2.7520.04511.2448222790.04594.1
2.75-2.9420.03815.9417521200.03894.1
2.94-3.1820.0414.4379419230.0492.5
3.18-3.4820.04312.1353317880.04392.4
3.48-3.891.90.0413.9313716180.0491.4
3.89-4.491.90.03616.4261013720.03688.1
4.49-5.51.90.03319.3233612060.03391.3
5.5-7.782.10.03818.119159080.03890.5
7.78-28.822.10.03917.49564510.03979.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.74→28.82 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.986 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.121
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. TWO NICKEL IONS IDENTIFIED BY X-RAY FLUORESCENCE AND ANOMALOUS DIFFERENCE FOURIERS ARE MODELED IN THE STRUCTURE. 5. RESIDUES FROM 133 TO 141, 208 TO 209 IN SUBUNIT A AND RESIDUES FROM 60 TO 61, 132 TO 140 IN SUBUNIT B ARE DISORDERED AND NOT MODELED IN THIS STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.215 2353 5 %RANDOM
Rwork0.175 ---
obs0.176 46725 94.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.462 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å21.49 Å2
2---1.84 Å20 Å2
3---2.34 Å2
Refinement stepCycle: LAST / Resolution: 1.74→28.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4016 0 2 230 4248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214194
X-RAY DIFFRACTIONr_bond_other_d0.0010.022796
X-RAY DIFFRACTIONr_angle_refined_deg1.6691.9445695
X-RAY DIFFRACTIONr_angle_other_deg1.14336784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2635536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1623.93201
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77115638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3571524
X-RAY DIFFRACTIONr_chiral_restr0.1280.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024832
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02920
X-RAY DIFFRACTIONr_nbd_refined0.2080.2841
X-RAY DIFFRACTIONr_nbd_other0.1990.22857
X-RAY DIFFRACTIONr_nbtor_refined0.1820.22071
X-RAY DIFFRACTIONr_nbtor_other0.0890.22179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2209
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.27
X-RAY DIFFRACTIONr_mcbond_it2.65132740
X-RAY DIFFRACTIONr_mcbond_other0.76431081
X-RAY DIFFRACTIONr_mcangle_it3.61454228
X-RAY DIFFRACTIONr_scbond_it6.01781648
X-RAY DIFFRACTIONr_scangle_it8.064111467
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 164 -
Rwork0.264 3308 -
all-3472 -
obs--95.2 %
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)
11.26850.1570.15142.6326-0.55271.2962-0.0097-0.0796-0.06810.1734-0.1102-0.31620.10340.0060.12-0.1242-0.0149-0.0297-0.11560.0538-0.108116.985527.154636.7775
21.7020.0524-0.27292.4713-0.10550.65880.06380.04620.044-0.2563-0.0825-0.2418-0.0902-0.09240.0187-0.10180.03470.037-0.10530.0385-0.144917.448956.657963.5149
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2732 - 274
2X-RAY DIFFRACTION2BB1 - 2732 - 274

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