[English] 日本語
Yorodumi
- PDB-3rza: Crystal structure of a tripeptidase (SAV1512) from staphylococcus... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rza
TitleCrystal structure of a tripeptidase (SAV1512) from staphylococcus aureus subsp. aureus mu50 at 2.10 A resolution
ComponentstripeptidaseTripeptide aminopeptidase
KeywordsHYDROLASE / PHOSPHORYLASE/HYDROLASE-LIKE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


aminopeptidase activity / metal ion binding
Similarity search - Function
Peptidase M20B, peptidase T-like / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Peptidase M42 / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 ...Peptidase M20B, peptidase T-like / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Peptidase M42 / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / ISOPROPYL ALCOHOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Similar to tripeptidase / Similar to tripeptidase
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a tripeptidase (SAV1512) from STAPHYLOCOCCUS AUREUS MU50 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Nov 16, 2011Group: Structure summary
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.5Feb 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tripeptidase
B: tripeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,87920
Polymers85,9472
Non-polymers1,93318
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6270 Å2
ΔGint-121 kcal/mol
Surface area29430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.996, 57.805, 79.857
Angle α, β, γ (deg.)89.670, 73.380, 72.360
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A2 - 375
2114B2 - 375
DetailsCRYSTAL PACKING AND SIZE EXCLUSION CHROMATOGRAPHY COUPLED WITH STATIC LIGHT SCATTERING ANALYSES SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein tripeptidase / Tripeptide aminopeptidase


Mass: 42973.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Mu50 / Gene: SAV1512 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q99TY1, UniProt: A0A0H3JRK2*PLUS

-
Non-polymers , 8 types, 415 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#6: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

-
Details

Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. CLEAVAGE OF ...THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. CLEAVAGE OF THE TAG WITH TEV PROTEASE LEAVES ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. HOWEVER, THE CLEAVAGE OF THE TAG WAS INCOMPLETE, LEAVING A MIXTURE OF PROTEIN WITH THE INTACT TAG AND CLEAVED TAG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.43
Details: 20.0% 2-propanol, 20.0% polyethylene glycol 4000, 0.1M sodium citrate - citric acid pH 5.43, Additive: 0.006 M zinc chloride, 0.006 M calcium chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97936,0.97911
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 12, 2010 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979361
30.979111
ReflectionResolution: 2.1→29.517 Å / Num. obs: 43307 / % possible obs: 88.6 % / Observed criterion σ(I): -3 / Redundancy: 1.99 % / Biso Wilson estimate: 24.476 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 4.89
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.09-2.160.6571.469246269173.4
2.16-2.250.4531.890608243187.4
2.25-2.350.408285607823187.9
2.35-2.480.3222.491288375188.3
2.48-2.630.2532.884417774189.1
2.63-2.830.1913.686968067190.1
2.83-3.120.1314.889858374190.2
3.12-3.570.09787748263191.7
3.57-4.490.05410.188358394192.6
4.49-29.250.04211.688838605194.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 30data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→29.517 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 8.892 / SU ML: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.177
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. RESIDUES 67-69 OF BOTH CHAINS WERE NOT MODELED DUE TO THE LACK OF ELECTRON DENSITY IN THIS REGION. 6. THE DI-METAL BINDING SITE IN THE PUTATIVE ACTIVE SITE HAS BEEN MODELED AS ONE ZINC (401) AND ONE CALCIUM (402) IN BOTH PROTOMERS. THE ASSIGNMENT OF ZINC WAS BASED ON THE PRESENCE OF AN ANOMALOUS DIFFERENCE FOURIER PEAK, COORDINATION GEOMETRY, FIT TO THE ELECTRON DENSITY AND THE CO-CRYSTALLIZATION ADDITIVE OF 0.006 M ZINC CHLORIDE. THE ASSIGNMENT OF CALCIUM FOR THE SECOND SITE WAS BASED ON THE ABSENCE OF AN ANOMALOUS DIFFERENCE FOURIER PEAK, COORDINATION GEOMETRY, FIT TO THE ELECTRON DENSITY AND THE CO-CRYSTALLIZATION ADDITIVE OF 0.006 M CALCIUM CHLORIDE. 7. ADDITIONAL CALCIUM IONS (CA), HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 8. CITRATE (CIT), 2-PROPANOL (IPA), AND POLYETHYLENE GLYCOL FRAGMENTS (PEG, PGE, PG4) FROM THE CRYSTALLIZATION AND CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 9. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 2176 5 %RANDOM
Rwork0.1668 ---
obs0.169 43307 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.84 Å2 / Biso mean: 25.5159 Å2 / Biso min: 9.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.1 Å20.14 Å2
2--0.12 Å2-0.29 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.517 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5529 0 111 397 6037
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225784
X-RAY DIFFRACTIONr_bond_other_d0.0050.023777
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9817836
X-RAY DIFFRACTIONr_angle_other_deg1.24239412
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98526.516221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.291151017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7771515
X-RAY DIFFRACTIONr_chiral_restr0.0810.2954
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026380
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02959
X-RAY DIFFRACTIONr_mcbond_it1.42733731
X-RAY DIFFRACTIONr_mcbond_other0.48531545
X-RAY DIFFRACTIONr_mcangle_it2.31556049
X-RAY DIFFRACTIONr_scbond_it3.50862053
X-RAY DIFFRACTIONr_scangle_it5.32281772
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4398 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.180.5
MEDIUM THERMAL0.772
LS refinement shellResolution: 2.095→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 140 -
Rwork0.234 2748 -
all-2888 -
obs--86.86 %
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)
11.00930.04080.03941.09040.19990.6333-0.00780.0123-0.12150.03150.01390.04220.06910.0354-0.00610.0777-0.0007-0.01160.1001-0.00410.040265.88218.95675.084
21.6596-0.61580.93740.6234-0.53051.5831-0.0559-0.06770.02320.0380.04610.0407-0.0485-0.09710.00980.0885-0.01170.01550.1225-0.02230.062337.98546.63972.574
31.15680.11160.18840.57570.1360.7015-0.0162-0.13910.080.022-0.01250.0168-0.06410.01710.02870.0985-0.0028-0.01140.1054-0.00490.046568.21831.18381.148
41.6116-2.46953.005119.009-4.16075.6342-0.05490.07980.12430.7829-0.1766-0.7822-0.10640.21010.23150.1964-0.0049-0.02810.23940.01870.077378.14421.88390.701
51.2902-0.03780.08620.89150.30481.0741-0.06680.2151-0.1212-0.0480.1308-0.0090.06780.1279-0.0640.0993-0.0004-0.00530.2258-0.03790.024713.65347.84631.684
62.054-0.86911.13671.3041-0.82181.60740.00430.10360.0262-0.0166-0.0527-0.0621-0.03440.09010.04850.0814-0.02090.00870.1403-0.01670.028141.21456.37158.004
71.79370.0135-0.15490.63010.19591.188-0.0150.04180.1463-0.00770.01720.0417-0.0970.0252-0.00220.1016-0.0019-0.01140.1714-0.00540.031110.86457.91440.18
86.9977-5.96451.38735.29090.580116.90970.15360.3460.2981-0.2605-0.314-0.2306-1.5393-1.50430.16030.24960.0948-0.0640.58410.08580.12310.80465.19227.245
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 180
2X-RAY DIFFRACTION1A401 - 402
3X-RAY DIFFRACTION2A181 - 290
4X-RAY DIFFRACTION3A291 - 366
5X-RAY DIFFRACTION4A367 - 375
6X-RAY DIFFRACTION5B0 - 180
7X-RAY DIFFRACTION5B401 - 402
8X-RAY DIFFRACTION6B181 - 290
9X-RAY DIFFRACTION7B291 - 366
10X-RAY DIFFRACTION8B367 - 375

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more