[English] 日本語
Yorodumi
- PDB-7ucv: The Crystal Structure of Apo Domain-Swapped Dimer Q108K:T51D:A28C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ucv
TitleThe Crystal Structure of Apo Domain-Swapped Dimer Q108K:T51D:A28CL36C R58:H:H:H:N59 HCRBPII with Histidine Insertion in the Hinge Loop Region at 2.19 Angstrom Resolution
ComponentsRetinol-binding protein 2
KeywordsLIPID BINDING PROTEIN / LBP / CRBPII
Function / homology
Function and homology information


vitamin A metabolic process / retinoid binding / retinal binding / retinol binding / epidermis development / fatty acid transport / Retinoid metabolism and transport / fatty acid binding / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin
Similarity search - Domain/homology
Retinol-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsGhanbarpour, A. / Geiger, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: The Crystal Structure of Domain-Sawpped Dimer Q108K:T51D:A28C:L36C:F57:H:R58 Mutant of hCRBPII with a Histidine Insertion in the Hinge Loop Region at 1.96 Angstrom Resolution
Authors: Ghanbarpour, A. / Geiger, J.
History
DepositionMar 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Retinol-binding protein 2
B: Retinol-binding protein 2


Theoretical massNumber of molelcules
Total (without water)32,0982
Polymers32,0982
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-36 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.952, 69.901, 107.254
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain 'A' and (resid 1 through 54 or resid 56 through 60 or resid 62 through 136))AA1 - 541 - 54
12THRTHRHISHIS(chain 'A' and (resid 1 through 54 or resid 56 through 60 or resid 62 through 136))AA56 - 6056 - 60
13ASNASNLYSLYS(chain 'A' and (resid 1 through 54 or resid 56 through 60 or resid 62 through 136))AA62 - 13662 - 136
21THRTHRTHRTHR(chain 'B' and (resid 1 through 54 or resid 56 through 60 or resid 62 through 136))BB1 - 541 - 54
22THRTHRHISHIS(chain 'B' and (resid 1 through 54 or resid 56 through 60 or resid 62 through 136))BB56 - 6056 - 60
23ASNASNLYSLYS(chain 'B' and (resid 1 through 54 or resid 56 through 60 or resid 62 through 136))BB62 - 13662 - 136

-
Components

#1: Protein Retinol-binding protein 2 / Cellular retinol-binding protein II / CRBP-II


Mass: 16048.979 Da / Num. of mol.: 2 / Mutation: A28C, L36C, T51D, Q111K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBP2, CRBP2
Production host: Bacterial expression vector pBEN1-SGC (others)
References: UniProt: P50120
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: PEG 4000, sodium acetate, ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.19→34.95 Å / Num. obs: 14150 / % possible obs: 94.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 23.31 Å2 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.101 / Net I/σ(I): 4.2
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.264 / Num. unique obs: 1272 / Rrim(I) all: 0.301 / % possible all: 85.2

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2rcq

2rcq


Resolution: 2.19→34.95 Å / SU ML: 0.2933 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.0363 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2664 1414 9.99 %
Rwork0.1982 12736 -
obs0.2051 14150 94.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.78 Å2
Refinement stepCycle: LAST / Resolution: 2.19→34.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 0 48 2298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742308
X-RAY DIFFRACTIONf_angle_d0.87213107
X-RAY DIFFRACTIONf_chiral_restr0.0563326
X-RAY DIFFRACTIONf_plane_restr0.0051401
X-RAY DIFFRACTIONf_dihedral_angle_d17.63811372
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.270.32511270.22721145X-RAY DIFFRACTION87.36
2.27-2.360.29191370.21351238X-RAY DIFFRACTION95.09
2.36-2.470.27671470.2141311X-RAY DIFFRACTION97.79
2.47-2.60.31761420.22111284X-RAY DIFFRACTION98.82
2.6-2.760.28151430.22011284X-RAY DIFFRACTION97.61
2.76-2.970.33371450.2231306X-RAY DIFFRACTION97.06
2.97-3.270.28361420.21881280X-RAY DIFFRACTION95.37
3.27-3.740.27881390.18431253X-RAY DIFFRACTION92.74
3.74-4.720.22431330.1641198X-RAY DIFFRACTION87.34
4.72-34.950.20241590.18131437X-RAY DIFFRACTION99.01
Refinement TLS params.Method: refined / Origin x: 27.8843129829 Å / Origin y: 26.6363513909 Å / Origin z: 12.9455735157 Å
111213212223313233
T0.201632911583 Å2-0.00403410402845 Å20.00340723388974 Å2-0.187780153511 Å20.024410363836 Å2--0.192815870685 Å2
L0.671158197348 °20.399912603027 °2-0.19549553032 °2-0.245137687588 °2-0.0917549438707 °2--0.0965316385726 °2
S-0.0488842895996 Å °0.0571912247913 Å °-0.00721384819309 Å °-0.0786093608741 Å °0.0304550733353 Å °-0.0221702405859 Å °0.0254564274674 Å °-0.00500680425637 Å °0.0147003751723 Å °
Refinement TLS groupSelection details: all

+
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