[English] 日本語
Yorodumi
- PDB-2olt: Crystal structure of a phou-like protein (so_3770) from shewanell... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2olt
TitleCrystal structure of a phou-like protein (so_3770) from shewanella oneidensis mr-1 at 2.00 A resolution
ComponentsHypothetical protein
KeywordsUNKNOWN FUNCTION / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyProtein of unknown function DUF47 / Putative phosphate transport regulator / Protein of unknown function DUF47 / Phosphate transport system protein phou homolog 2; domain 2 / PhoU-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / TIGR00153 family protein
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of NP_719307.1 from Shewanella oneidensis at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Remark 300 BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,12710
Polymers77,6523
Non-polymers4757
Water6,864381
1
B: Hypothetical protein
C: Hypothetical protein
hetero molecules

B: Hypothetical protein
C: Hypothetical protein
hetero molecules

B: Hypothetical protein
C: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,34621
Polymers155,3046
Non-polymers1,04215
Water1086
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
Buried area17090 Å2
ΔGint-151 kcal/mol
Surface area50930 Å2
MethodPISA
2
A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,04612
Polymers103,5364
Non-polymers5108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area17590 Å2
ΔGint-132 kcal/mol
Surface area50020 Å2
MethodPISA
3
A: Hypothetical protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)156,06918
Polymers155,3046
Non-polymers76512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)99.530, 99.530, 395.920
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41A
51B
61C
71A
81B
91C
101A
111B
121C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROLEULEU2AA14 - 7015 - 71
21PROPROLEULEU2BB14 - 7015 - 71
31PROPROLEULEU2CC14 - 7015 - 71
42THRTHRVALVAL1AA71 - 8072 - 81
52THRTHRVALVAL1BB71 - 8072 - 81
62THRTHRVALVAL1CC71 - 8072 - 81
73GLUGLUGLUGLU2AA81 - 14782 - 148
83GLUGLUGLUGLU2BB81 - 14782 - 148
93GLUGLUGLUGLU2CC81 - 14782 - 148
104ARGARGVALVAL2AA153 - 226154 - 227
114ARGARGVALVAL2BB153 - 226154 - 227
124ARGARGVALVAL2CC153 - 226154 - 227
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A HEXAMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Hypothetical protein


Mass: 25884.010 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: NP_719307.1, SO_3770 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8EAX1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4349.37
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop6.8NANODROP, 1.5M Sodium acetate, 0.1M Sodium cacodylate pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop6.5NANODROP, 1.0M Sodium citrate, 0.1M Sodium cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.211
SYNCHROTRONSSRL BL11-120.918370, 0.979318, 0.979035
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDSep 14, 2006
ADSC QUANTUM 3152CCDMay 7, 2006Flat mirror (vertical focusing)
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1Single crystal Si(111) bent (horizontal focusing)
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.918371
30.9793181
40.9790351
ReflectionResolution: 2→29.16 Å / Num. obs: 51605 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.058 / Χ2: 0.995 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.055.50.62336301.081,2100
2.05-2.115.50.50536520.9721,2100
2.11-2.175.50.37236491.0041,2100
2.17-2.245.60.336430.9631,2100
2.24-2.325.50.23536540.9191,2100
2.32-2.415.60.18436521.0191,2100
2.41-2.525.60.14536500.9471,2100
2.52-2.655.50.10136761.0091,2100
2.65-2.825.50.08336760.9861,2100
2.82-3.045.50.06736740.9211,2100
3.04-3.345.50.05737141.0131,2100
3.34-3.835.50.05237181.1011,2100
3.83-4.825.40.04337620.9371,299.9
4.82-505.20.02938551.061,298.4

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
DENZOdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2→29.16 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.832 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.163
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ELECTRON DENSITY SHOWS THAT RESIDUES 0-12 OF THE A SUBUNIT, RESIDUES 0-13 OF THE B SUBUNIT AND FOR RESIDUES 0-7 OF THE C SUBUNIT ARE DISORDERED. THEREFORE THESE RESIDUES WERE NOT MODELED. ELECTRON DENSITIES FOR THE FOLLOWING REGIONS ARE ALSO DISORDERED AND WERE NOT MODELED: B149-B150, C73-C74. 5. GLYCEROL MOLECULES USED AS A CRYOPROTECTANT HAVE BEEN INCORPORATED INTO THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2634 5.1 %RANDOM
Rwork0.203 ---
all0.205 ---
obs0.205 51591 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.759 Å2
Baniso -1Baniso -2Baniso -3
1-2.45 Å21.22 Å20 Å2
2--2.45 Å20 Å2
3----3.67 Å2
Refinement stepCycle: LAST / Resolution: 2→29.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4898 0 27 381 5306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225012
X-RAY DIFFRACTIONr_bond_other_d0.0030.024781
X-RAY DIFFRACTIONr_angle_refined_deg1.5651.9876783
X-RAY DIFFRACTIONr_angle_other_deg1.006311050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9815645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87325.433208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75315902
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5451532
X-RAY DIFFRACTIONr_chiral_restr0.1090.2810
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025524
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02910
X-RAY DIFFRACTIONr_nbd_refined0.2320.31289
X-RAY DIFFRACTIONr_nbd_other0.1620.34809
X-RAY DIFFRACTIONr_nbtor_refined0.1860.52569
X-RAY DIFFRACTIONr_nbtor_other0.0930.53049
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1970.5489
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0210.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.3123
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.546
X-RAY DIFFRACTIONr_mcbond_it0.9561.53313
X-RAY DIFFRACTIONr_mcbond_other0.2121.51306
X-RAY DIFFRACTIONr_mcangle_it1.35325164
X-RAY DIFFRACTIONr_scbond_it2.45931897
X-RAY DIFFRACTIONr_scangle_it3.8154.51617
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1252TIGHT POSITIONAL0.070.05
2B1252TIGHT POSITIONAL0.060.05
3C1252TIGHT POSITIONAL0.080.05
1A1770MEDIUM POSITIONAL0.420.5
2B1770MEDIUM POSITIONAL0.360.5
3C1770MEDIUM POSITIONAL0.330.5
1A1252TIGHT THERMAL0.170.5
2B1252TIGHT THERMAL0.160.5
3C1252TIGHT THERMAL0.150.5
1A1770MEDIUM THERMAL0.682
2B1770MEDIUM THERMAL0.692
3C1770MEDIUM THERMAL0.582
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 205 -
Rwork0.252 3564 -
obs-3769 99.87 %
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)
11.86120.0318-0.14432.09640.23533.6908-0.06450.16960.1052-0.1405-0.05740.0645-0.554-0.03010.122-0.1373-0.0308-0.0187-0.29080.018-0.1384.130317.656427.5364
20.93890.06670.23810.98290.31863.8182-0.06150.09040.0229-0.1153-0.0043-0.081-0.07840.57650.0658-0.1479-0.021-0.0113-0.09540.0298-0.086414.3276.450130.4636
32.04830.24531.73011.2518-0.00295.9853-0.1475-0.36490.15560.2059-0.05550.1256-0.3925-0.65360.203-0.2052-0.0108-0.0025-0.0616-0.027-0.056131.728127.7671-12.9376
41.6402-0.1067-0.16851.41120.11174.8934-0.0589-0.1561-0.16050.1170.01310.06920.6364-0.16620.0458-0.0881-0.04460.0038-0.1199-0.02540.025540.921116.0886-16.5371
51.59530.62510.62371.7584-0.30775.0167-0.0608-0.0529-0.2237-0.1368-0.0847-0.0130.8784-0.62620.1456-0.0475-0.1570.00850.0348-0.0063-0.076436.126715.765441.5161
60.4137-0.16790.1340.93760.49486.6244-0.05840.11780.0047-0.1476-0.06260.1429-0.4466-1.14120.121-0.04960.0143-0.02530.2289-0.0249-0.053934.189230.627145.0452
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA13 - 11314 - 114
22AA114 - 226115 - 227
33BB14 - 11315 - 114
44BB114 - 226115 - 227
55CC8 - 1139 - 114
66CC114 - 226115 - 227

+
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