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- PDB-3iib: Crystal structure of Peptidase M28 precursor (YP_926796.1) from S... -

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Basic information

Entry
Database: PDB / ID: 3iib
TitleCrystal structure of Peptidase M28 precursor (YP_926796.1) from SHEWANELLA AMAZONENSIS SB2B at 1.70 A resolution
ComponentsPeptidase M28
KeywordsHYDROLASE / YP_926796.1 / Peptidase M28 precursor / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Peptidase family M28
Function / homology
Function and homology information


metallodipeptidase activity / carboxypeptidase activity / lysosome / metal ion binding
Similarity search - Function
Carboxypeptidase Q / Glucose Oxidase; domain 1 - #30 / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(bba) Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Carboxypeptidase Q
Similarity search - Component
Biological speciesShewanella amazonensis SB2B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Peptidase M28 precursor (YP_926796.1) from SHEWANELLA AMAZONENSIS SB2B at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: 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 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase M28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1056
Polymers47,6111
Non-polymers4935
Water11,367631
1
A: Peptidase M28
hetero molecules

A: Peptidase M28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,20912
Polymers95,2232
Non-polymers98610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4030 Å2
ΔGint-145 kcal/mol
Surface area32300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.442, 84.867, 80.114
Angle α, β, γ (deg.)90.000, 115.850, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-480-

HOH

21A-621-

HOH

31A-629-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein Peptidase M28


Mass: 47611.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella amazonensis SB2B (bacteria) / Gene: Sama_0919, YP_926796.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A1S420
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 631 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT INCLUDING RESIDUES 25-467 WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...THIS CONSTRUCT INCLUDING RESIDUES 25-467 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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M MgCl2, 30.0000% PEG-400, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97791
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.977911
ReflectionResolution: 1.7→29.374 Å / Num. obs: 58230 / % possible obs: 97.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 10.978 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.742.60.4621.91109042390.46296
1.74-1.792.60.4012.21078441170.40196.1
1.79-1.842.60.3312.71056240250.33196.4
1.84-1.92.60.2883.21026139200.28896.6
1.9-1.962.60.2414996138000.24196.8
1.96-2.032.60.2034.8960036710.20397
2.03-2.112.60.1745.7944836180.17497.2
2.11-2.192.60.1556.5889934000.15597.3
2.19-2.292.60.1377.4880233700.13797.6
2.29-2.42.60.128.3821231580.1297.9
2.4-2.532.60.1099.2784330100.10997.8
2.53-2.692.60.10110.1743128540.10198.1
2.69-2.872.60.0911.3701926970.0998.2
2.87-3.12.60.07813.3660425470.07898.4
3.1-3.42.60.0715.3598523080.0798.6
3.4-3.82.60.06317.2543421140.06398.7
3.8-4.392.60.06618.6484218650.06699
4.39-5.382.60.06918.8406915870.06999.2
5.38-7.62.50.0816.7316512510.0899.4
7.6-29.372.50.0632016936790.06397.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.374 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.559 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.086
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.ZINC (ZN) HAS BEEN MODELED AT THE PUTATIVE ACTIVE SITE BASED ON A FLUORESCENCE EXCITATION SCAN AND THE ANOMALOUS DIFFERENCE FOURIER MAP. 5.THERE IS A CIS-PEPTIDE BOND BETWEEN RESIDUES ASP292 AND ASP293 AT THE PUTATIVE ACTIVE SITE. 6.PEG FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 2960 5.1 %RANDOM
Rwork0.151 ---
obs0.152 58229 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.74 Å2 / Biso mean: 11.122 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å2-0.34 Å2
2---0.17 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 24 631 3938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223459
X-RAY DIFFRACTIONr_bond_other_d0.0010.022302
X-RAY DIFFRACTIONr_angle_refined_deg1.4711.9664721
X-RAY DIFFRACTIONr_angle_other_deg0.90935676
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4485474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.00124.965143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63615567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.141519
X-RAY DIFFRACTIONr_chiral_restr0.0870.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213938
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02640
X-RAY DIFFRACTIONr_mcbond_it1.6432244
X-RAY DIFFRACTIONr_mcbond_other0.533916
X-RAY DIFFRACTIONr_mcangle_it2.46653611
X-RAY DIFFRACTIONr_scbond_it4.04881215
X-RAY DIFFRACTIONr_scangle_it6.271111093
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 207 -
Rwork0.238 4019 -
all-4226 -
obs--95.91 %
Refinement TLS params.Method: refined / Origin x: 1.1964 Å / Origin y: 12.5565 Å / Origin z: 20.4912 Å
111213212223313233
T0.0087 Å2-0.0009 Å20.0051 Å2-0.0022 Å20.0022 Å2--0.0156 Å2
L0.1584 °20.077 °20.1582 °2-0.1537 °20.0697 °2--0.4015 °2
S0.0067 Å °-0.0107 Å °0.0111 Å °0.0196 Å °-0.0026 Å °0.0042 Å °0.0133 Å °-0.0245 Å °-0.004 Å °

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