[English] 日本語
Yorodumi
- PDB-2h1j: 3.1 A X-ray structure of putative Oligoendopeptidase F: Crystals ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h1j
Title3.1 A X-ray structure of putative Oligoendopeptidase F: Crystals grown by microfluidic seeding
ComponentsOligoendopeptidase F
KeywordsHYDROLASE / Structural Genomics / microfluidic seeding / PSI-2 / Protein Structure Initiative / ACCELERATED TECHNOLOGIES CENTER FOR GENE TO 3D STRUCTURE / ATCG3D
Function / homology
Function and homology information


peptide metabolic process / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M3B, oligoendopeptidase-related / Neurolysin; domain 3 - #30 / Peptidase M3A/M3B catalytic domain / Peptidase M3A/M3B / Peptidase family M3 / Neurolysin; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Oligoendopeptidase F
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsGerdts, C.J. / Tereshko, V. / Dementieva, I. / Collart, F. / Joachimiak, A. / Kossiakoff, A. / Ismagilov, R.F. / Accelerated Technologies Center for Gene to 3D Structure (ATCG3D)
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: Time-Controlled Microfluidic Seeding in nL-Volume Droplets To Separate Nucleation and Growth Stages of Protein Crystallization.
Authors: Gerdts, C.J. / Tereshko, V. / Yadav, M.K. / Dementieva, I. / Collart, F. / Joachimiak, A. / Stevens, R.C. / Kuhn, P. / Kossiakoff, A. / Ismagilov, R.F.
History
DepositionMay 16, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). EACH CHAIN REPRESENTS ONE BIOLOGICAL UNIT. THE OLIGOMERIZATION IS UNKNOWN.
Remark 999At the time of processing, the sequence of this protein is not available at the UNP sequence ...At the time of processing, the sequence of this protein is not available at the UNP sequence database. Residues -2 to 0 are cloning artifacts.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Oligoendopeptidase F
B: Oligoendopeptidase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,1204
Polymers133,9902
Non-polymers1312
Water362
1
A: Oligoendopeptidase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0602
Polymers66,9951
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oligoendopeptidase F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0602
Polymers66,9951
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.324, 119.324, 248.736
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSPHEAA2 - 275 - 30
21LYSPHEBB2 - 275 - 30
32GLYLEUAA31 - 3534 - 38
42GLYLEUBB31 - 3534 - 38
53ILETYRAA43 - 9146 - 94
63ILETYRBB43 - 9146 - 94
74LYSGLYAA110 - 211113 - 214
84LYSGLYBB110 - 211113 - 214
95PHEALAAA215 - 319218 - 322
105PHEALABB215 - 319218 - 322
116LYSASNAA323 - 376326 - 379
126LYSASNBB323 - 376326 - 379
137PROILEAA378 - 480381 - 483
147PROILEBB378 - 480381 - 483
158TYRASPAA481 - 489484 - 492
168TYRASPBB481 - 489484 - 492
179TYRLEUAA490 - 564493 - 567
189TYRLEUBB490 - 564493 - 567
DetailsThis entry contains the crystallographic asymmetic unit which consists of 2 chain(s). Each chain represents one biological unit. The oligomerization is unknown.

-
Components

#1: Protein Oligoendopeptidase F


Mass: 66994.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: GK0963 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5L1D2*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 296 K / pH: 7
Details: PRECIPITATION FROM A HANGING DROP VAPOR DIFFUSION TRIAL (60% TASCIMATE IN BIS-TRIS PROPANE PH= 7.0) WAS USED TO SEED INTO A 45% TASCIMATE SOLUTION USING A MICROFLUIDIC MICROBATCH SEEDING ...Details: PRECIPITATION FROM A HANGING DROP VAPOR DIFFUSION TRIAL (60% TASCIMATE IN BIS-TRIS PROPANE PH= 7.0) WAS USED TO SEED INTO A 45% TASCIMATE SOLUTION USING A MICROFLUIDIC MICROBATCH SEEDING TECHNIQUE. CONCENTRATION OF PROTEIN WAS 17 MG/ML., TEMPERATURE 296K , pH 7.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 1, 2006 / Details: ADJUSTABLE FOCUSING MIRRORS. K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 37927 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 9.28
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.88 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 3.1→20 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.927 / SU B: 34.316 / SU ML: 0.263 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.363 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WE HAVE DETECTED THE DIFFERENCE ELECTRON DENSITY AT >2.0 SIGMA LEVEL IN THE CENTER GROOVE OF THE MOLECULE. WE HAVE USED TASCIMATE (THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WE HAVE DETECTED THE DIFFERENCE ELECTRON DENSITY AT >2.0 SIGMA LEVEL IN THE CENTER GROOVE OF THE MOLECULE. WE HAVE USED TASCIMATE (THE HAMPTON RESEARCH PROPRIETARY MIXTURE OF ORGANIC ACIDS) FOR CRYSTALLIZATION. IT IS LIKELY THAT ONE OF THE ORGANIC ACIDS OR THEIR MIXTURE ENTERS THE GROOVE IN THE SOLUTION AND HELPS TO STABILIZE THE CLOSED CONFORMATION OF OLIGOENDOPEPTIDASE F IN THE CRYSTAL FORM. WE DID NOT ATTEMPT TO INTERPRET THE DIFFERENCE DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.22529 1892 5 %RANDOM
Rwork0.18735 ---
obs0.18923 35830 99.96 %-
all-31069 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 69.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 3.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9337 0 2 2 9341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.029601
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1311.87912979
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21351127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29123.333534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.015151590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9021582
X-RAY DIFFRACTIONr_chiral_restr0.0790.21313
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027592
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.24607
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.26628
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2234
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.239
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2981.55739
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.43929045
X-RAY DIFFRACTIONr_scbond_it0.77534394
X-RAY DIFFRACTIONr_scangle_it1.1334.53934
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
2112tight positional0.030.05
2245medium positional0.290.5
2112tight thermal0.040.5
2245medium thermal0.262
LS refinement shellResolution: 3.1→3.182 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 151 -
Rwork0.293 2547 -
obs--99.78 %
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)
11.32480.29410.46680.97110.11031.2241-0.01390.0570.23850.0342-0.107-0.0312-0.3508-0.14460.1209-0.04740.09720.0498-0.1992-0.0332-0.098341.184432.1445103.8196
20.679-0.40180.26061.7648-0.53850.96140.0605-0.105-0.11070.0994-0.04210.14720.1163-0.2816-0.0184-0.1839-0.1190.0591-0.0592-0.0465-0.149991.51483.4823111.4293
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 564
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION1A602
4X-RAY DIFFRACTION2B1 - 564
5X-RAY DIFFRACTION2B701
6X-RAY DIFFRACTION2B702

+
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://pdbjlvh1.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