[English] 日本語
Yorodumi
- PDB-3bn8: Crystal structure of a putative sterol carrier protein type 2 (af... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bn8
TitleCrystal structure of a putative sterol carrier protein type 2 (af1534) from archaeoglobus fulgidus dsm 4304 at 2.11 A resolution
ComponentsPutative sterol carrier protein 2
KeywordsTRANSPORT PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySCP2 sterol-binding domain / SCP-2 sterol transfer family / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / 2-Layer Sandwich / Alpha Beta / Unknown ligand / SCP2 domain-containing protein
Function and homology information
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.11 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative sterol carrier protein 2 (2649030) from Archaeoglobus fulgidus at 2.11 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Jan 25, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.6Nov 13, 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 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. POSITIONS 39 AND 40 ... SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH. POSITIONS 39 AND 40 WERE MUTATED FROM GLU TO TYR BASED ON RESULTS FROM THE UCLA SURFACE ENTROPY REDUCTION SERVER.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative sterol carrier protein 2
B: Putative sterol carrier protein 2


Theoretical massNumber of molelcules
Total (without water)30,0543
Polymers30,0542
Non-polymers01
Water1,22568
1
A: Putative sterol carrier protein 2

A: Putative sterol carrier protein 2


Theoretical massNumber of molelcules
Total (without water)30,0544
Polymers30,0542
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area3270 Å2
MethodPISA
2
B: Putative sterol carrier protein 2

B: Putative sterol carrier protein 2


Theoretical massNumber of molelcules
Total (without water)30,0542
Polymers30,0542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area3360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.250, 105.210, 85.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-118-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

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
11SERSERALAALA4AA2 - 10014 - 112
21SERSERALAALA4BB2 - 10014 - 112
32GLNGLNGLNGLN6AA101 - 111113 - 123
42GLNGLNGLNGLN6BB101 - 111113 - 123
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Putative sterol carrier protein 2


Mass: 15027.056 Da / Num. of mol.: 2 / Mutation: E39Y, E40Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126 / Gene: 2649030, AF_1534 / Plasmid: MH4a / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: O28738
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: NANODROP, 20.0% PEG 1000, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.91840, 0.97953, 0.97939
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 26, 2007 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
20.979531
30.979391
ReflectionResolution: 2.1→28.571 Å / Num. obs: 14873 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 41.746 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 12.16
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.170.2313.243682622198.3
2.17-2.260.1694.250972931199
2.26-2.360.135.448572791199.3
2.36-2.490.1216.351592894198.9
2.49-2.640.097.848852707199.1
2.64-2.850.071052282881197.9
2.85-3.130.0491450312752197.8
3.13-3.590.03519.752592791197.1
3.59-4.510.02824.551452728196.3
4.51-28.5710.02427.551072663192.8

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
SHARPphasing
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.11→28.571 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.93 / SU B: 10.274 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.193
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. ONE UNKNOWN LIGAND IS MODELED IN THE STRUCTURE NEAR RESIDUE TYR 45. 5. UNKNOWN ELECTRON DENSITY AROUND RESIDUE 5 IS NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.248 757 5.1 %RANDOM
Rwork0.196 ---
obs0.198 14854 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.64 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å20 Å2
2--2.99 Å20 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 2.11→28.571 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1747 0 9 68 1824
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221808
X-RAY DIFFRACTIONr_bond_other_d0.0010.021211
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9422439
X-RAY DIFFRACTIONr_angle_other_deg0.90232956
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4085228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.37624.93881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63615302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.925154
X-RAY DIFFRACTIONr_chiral_restr0.0960.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02374
X-RAY DIFFRACTIONr_nbd_refined0.2170.3332
X-RAY DIFFRACTIONr_nbd_other0.1850.31163
X-RAY DIFFRACTIONr_nbtor_refined0.1920.5879
X-RAY DIFFRACTIONr_nbtor_other0.0920.5858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.5106
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.326
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.339
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2610.56
X-RAY DIFFRACTIONr_mcbond_it2.44231178
X-RAY DIFFRACTIONr_mcbond_other0.7263467
X-RAY DIFFRACTIONr_mcangle_it3.26351794
X-RAY DIFFRACTIONr_scbond_it5.4068769
X-RAY DIFFRACTIONr_scangle_it6.76911645
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
1277MEDIUM POSITIONAL0.40.5
142LOOSE POSITIONAL1.645
1277MEDIUM THERMAL1.222
142LOOSE THERMAL2.9610
LS refinement shellResolution: 2.11→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 52 -
Rwork0.218 1036 -
all-1088 -
obs--98.37 %
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)
12.02370.2494-0.22240.6670.62263.87720.0843-0.1034-0.0383-0.0684-0.15780.09860.146-0.76630.0735-0.1113-0.0295-0.04070.0331-0.0176-0.135316.844546.58532.875
22.1398-0.12390.40671.9083-0.72333.04570.1422-0.1652-0.15950.1737-0.0549-0.36560.35420.3974-0.0873-0.06720.0376-0.0607-0.08410.0297-0.019841.999842.623248.3442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-2 - 11310 - 125
2X-RAY DIFFRACTION2BB2 - 11114 - 123

+
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