[English] 日本語
Yorodumi
- PDB-3mnf: Crystal structure of PAC2 family protein from Streptomyces avermi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mnf
TitleCrystal structure of PAC2 family protein from Streptomyces avermitilis MA
ComponentsPAC2 family protein
Keywordsstructural genomics / unknown function / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyRv2714-like / PAC-like subunit / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Carboxylate--amine ligase
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.97 Å
AuthorsChang, C. / Hatzos, C. / Morgan, T. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of PAC2 family protein from Streptomyces avermitilis MA
Authors: Chang, C. / Hatzos, C. / Morgan, T. / Bearden, J. / Joachimiak, A.
History
DepositionApr 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_comp_id / _struct_conn.ptnr2_label_seq_id / _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: PAC2 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4172
Polymers27,3811
Non-polymers351
Water00
1
A: PAC2 family protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)164,50012
Polymers164,2886
Non-polymers2136
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area15220 Å2
ΔGint-127 kcal/mol
Surface area61860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.943, 143.943, 81.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Detailshexamer with operators (x,y,z), (-y+1,x-y,z), (-x+y+1,-x+1,z), (-y+1,-x+1,-z+1/2), (x,x-y,-z+1/2), (-x+y+1,y,-z+1/2)

-
Components

#1: Protein PAC2 family protein


Mass: 27381.268 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: SAV6650, SAV_6650 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q828L9
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.43 Å3/Da / Density % sol: 72.23 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.0M Na/K tartrate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. all: 11041 / Num. obs: 10559 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 12.6 % / Biso Wilson estimate: 76.6 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 41.5
Reflection shellResolution: 3→3.05 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.847 / Mean I/σ(I) obs: 4.84 / Num. unique all: 507 / % possible all: 100

-
Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.97→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.919 / SU B: 26.757 / SU ML: 0.232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.5 / ESU R Free: 0.306
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24108 502 4.8 %RANDOM
Rwork0.21572 ---
all0.21696 10484 --
obs0.21696 10484 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 88.778 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å2-0.37 Å20 Å2
2---0.74 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 2.97→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 1 0 1748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221790
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9542459
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4855233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.3523.91974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27215246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4611512
X-RAY DIFFRACTIONr_chiral_restr0.0930.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211391
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.541.51171
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04621871
X-RAY DIFFRACTIONr_scbond_it1.5573619
X-RAY DIFFRACTIONr_scangle_it2.7164.5588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.975→3.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 28 -
Rwork0.236 668 -
obs-696 98.31 %
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)
15.0159-1.74120.20983.58141.114.6110.2128-0.2480.09940.19270.06810.2842-0.1055-0.7718-0.28090.12130.07340.14230.20780.08790.210653.809255.719834.435
23.80023.219-3.51778.0211-1.92393.5528-0.01560.25350.05190.32380.10690.65450.1144-0.4026-0.09130.1507-0.0405-0.01930.34320.1940.459855.423737.720435.2197
34.4827-0.73770.95363.757-1.04513.94330.10740.20420.4282-0.21430.06480.1238-0.2607-0.5534-0.17220.15160.09520.11810.18950.05180.185457.063756.797827.1985
45.2642-1.1249-0.50342.89980.30934.94790.0327-0.60420.930.43140.254-0.1885-0.8988-0.2183-0.28670.40080.11240.16920.1759-0.10280.336761.190466.641140.5754
56.4154-0.68325.57756.31370.094913.36850.0383-1.63390.53151.79040.03691.1712-0.4417-1.4633-0.07520.76990.27520.46110.9917-0.11340.376149.318963.4455.2009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 52
2X-RAY DIFFRACTION2A53 - 75
3X-RAY DIFFRACTION3A76 - 119
4X-RAY DIFFRACTION4A120 - 214
5X-RAY DIFFRACTION5A215 - 256

+
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