[English] 日本語
Yorodumi
- PDB-2pgc: Crystal structure of a a marine metagenome protein (jcvi_pep_1096... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2pgc
TitleCrystal structure of a a marine metagenome protein (jcvi_pep_1096685590403) from uncultured marine organism at 2.53 A resolution
Componentsuncharacterized protein
KeywordsUNKNOWN FUNCTION / Metagenomics target / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyAlpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Function and homology information
Biological speciesuncultured marine organism (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.53 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of uncharacterized protein (JCVI_PEP_1096685590403) from an environmental metagenome (unidentified marine microbe), Sorcerer II Global Ocean Sampling experiment at 2.53 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 5 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 5 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A PENTAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.
Remark 999 SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE 1. THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE, FOLLOWED BY THE TARGET SEQUENCE. 2. THE SEQUENCE OF THE PROTEIN WAS NOT AVAILABLE IN THE UNIPROT DATABASE AT THE TIME OF DEPOSITION. 3. THE PRODUCT OF THE EXPRESSED SYNTHETIC GENE WAS BASED ON THE PREDICTED SEQUENCE OF ACCESSION ID JCVI_PEP_1096685590403 FROM THE J. CRAIG VENTER INSTITUTE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein
C: uncharacterized protein
D: uncharacterized protein
E: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,32511
Polymers117,1125
Non-polymers2136
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-120 kcal/mol
Surface area41980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.475, 139.935, 60.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23E
14A
24C
34A
44C
54A
64C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLEULEU2AA2 - 2063 - 207
211SERSERLEULEU2BB2 - 2063 - 207
112SERSERLEULEU2AA2 - 2063 - 207
212SERSERLEULEU2DD2 - 2063 - 207
113SERSERLEULEU2AA2 - 2063 - 207
213SERSERLEULEU2EE2 - 2063 - 207
114SERSERASPASP2AA2 - 153 - 16
214ILEILEASPASP2CC4 - 155 - 16
324PHEPHESERSER4AA16 - 2817 - 29
424PHEPHESERSER4CC16 - 2817 - 29
534TYRTYRLEULEU2AA29 - 20630 - 207
634TYRTYRLEULEU2CC29 - 20630 - 207

NCS ensembles :
ID
1
2
3
4
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A PENTAMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

-
Components

#1: Protein
uncharacterized protein


Mass: 23422.406 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured marine organism (environmental samples)
Gene: SYNTHETIC GENE: The gene product was based on JCVI_PEP_1096685590403 from the Sorcerer II Global Ocean Sampling experiment
Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: NANODROP, 0.2M K2SO4, 20.0% PEG 3350, No Buffer pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97949
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2007 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979491
ReflectionResolution: 2.53→29.921 Å / Num. obs: 39917 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 62.23 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.53-2.63.60.6841.11027628840.68499.6
2.6-2.673.60.551.41010628240.5599.9
2.67-2.743.60.461.7997127630.4699.7
2.74-2.833.60.3782955226530.37899.8
2.83-2.923.60.2852946826230.28599.8
2.92-3.023.70.2243.2921025220.22499.7
3.02-3.143.70.172.7883624200.1799.9
3.14-3.273.70.1355.6871523660.13599.9
3.27-3.413.70.116.7836622640.11100
3.41-3.583.70.0848.3806921810.084100
3.58-3.773.70.06810.2755720520.068100
3.77-43.70.05811.7717219550.058100
4-4.283.70.04714.2679918500.047100
4.28-4.623.70.04513.8630017240.045100
4.62-5.063.60.04613.2586816090.046100
5.06-5.663.60.04514.3521214440.04599.9
5.66-6.533.60.05212.2465512970.05299.9
6.53-83.50.05411.2388411080.05499.9
8-11.313.40.0391629928780.03999.8
11.31-29.923.10.03615.415485000.03694.6

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0019refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MAR345CCDdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.53→29.921 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 22.221 / SU ML: 0.235 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.648 / ESU R Free: 0.292
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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. DENSITY BLOBS OUTSIDE PROTEIN ARE LEFT UNINTEPRETED DUE TO LIMITED RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2000 5 %RANDOM
Rwork0.214 ---
all0.215 ---
obs0.215 39877 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 53.528 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.71 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.53→29.921 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7857 0 6 131 7994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228021
X-RAY DIFFRACTIONr_bond_other_d0.0020.025260
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.96110844
X-RAY DIFFRACTIONr_angle_other_deg0.867312864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.04251027
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65224.399341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.081151372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9591534
X-RAY DIFFRACTIONr_chiral_restr0.0710.21243
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029014
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021660
X-RAY DIFFRACTIONr_nbd_refined0.2080.21535
X-RAY DIFFRACTIONr_nbd_other0.1840.24938
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23973
X-RAY DIFFRACTIONr_nbtor_other0.0860.24429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2196
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0030.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.24
X-RAY DIFFRACTIONr_mcbond_it1.49235458
X-RAY DIFFRACTIONr_mcbond_other0.4532103
X-RAY DIFFRACTIONr_mcangle_it2.36658135
X-RAY DIFFRACTIONr_scbond_it4.02383259
X-RAY DIFFRACTIONr_scangle_it5.075112705
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
11210TIGHT POSITIONAL0.050.05
11383MEDIUM POSITIONAL0.190.5
11210TIGHT THERMAL0.120.5
11383MEDIUM THERMAL0.672
21208TIGHT POSITIONAL0.050.05
21367MEDIUM POSITIONAL0.350.5
21208TIGHT THERMAL0.130.5
21367MEDIUM THERMAL0.712
31208TIGHT POSITIONAL0.050.05
31331MEDIUM POSITIONAL0.330.5
31208TIGHT THERMAL0.110.5
31331MEDIUM THERMAL0.832
41119TIGHT POSITIONAL0.050.05
41406MEDIUM POSITIONAL0.390.5
41119TIGHT THERMAL0.110.5
41406MEDIUM THERMAL0.712
LS refinement shellResolution: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 144 -
Rwork0.294 2738 -
obs-2882 99.52 %
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)
11.3053-0.6174-0.59220.33290.32310.8643-0.0467-0.0528-0.22410.05680.18210.10880.264-0.0457-0.1354-0.0219-0.038-0.0249-0.11220.0242-0.038298.059684.468619.9095
20.936-0.0879-0.39031.71280.60281.11660.05580.1874-0.1039-0.22750.03870.32540.141-0.0741-0.0945-0.1392-0.0457-0.0397-0.03740.0117-0.053981.4522103.24345.9128
31.8201-0.72390.95592.3789-0.95271.3953-0.1103-0.01090.31980.387-0.0734-0.3506-0.31020.1930.1837-0.0107-0.0876-0.01420.0490.01220.0924121.1111125.703617.2846
40.57680.75840.48253.09190.24260.9173-0.17510.15470.0562-0.22820.14830.0353-0.0630.04580.0268-0.0421-0.03070.0095-0.08970.0522-0.138795.5594129.34465.155
52.13531.25890.50692.8342-0.0241.68680.07630.1194-0.15910.20340.0331-0.4015-0.00870.2728-0.1094-0.13060.042-0.0883-0.0184-0.0474-0.0592123.184297.935526.9145
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA0 - 2061 - 207
22BB2 - 2063 - 207
33CC4 - 2065 - 207
44DD2 - 2063 - 207
55EE2 - 2063 - 207

+
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