[English] 日本語
Yorodumi
- PDB-4a60: Crystal structure of human testis-specific fatty acid binding pro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a60
TitleCrystal structure of human testis-specific fatty acid binding protein 9 (FABP9)
ComponentsFATTY ACID-BINDING PROTEIN 9 TESTIS LIPID-BINDING PROTEIN, TLBP, TESTIS-TYPE FATTY ACID-BINDING PROTEIN, T-FABP
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


long-chain fatty acid binding / Triglyceride catabolism / long-chain fatty acid transport / nucleus / cytosol
Similarity search - Function
Cytosolic fatty-acid binding proteins signature. / Intracellular lipid binding protein / Cytosolic fatty-acid binding / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Fatty acid-binding protein 9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 Å
AuthorsMuniz, J.R.C. / Kiyani, W. / Shrestha, L. / Froese, D.S. / Krojer, T. / Vollmar, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. ...Muniz, J.R.C. / Kiyani, W. / Shrestha, L. / Froese, D.S. / Krojer, T. / Vollmar, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / von Delft, F. / Yue, W.W.
CitationJournal: To be Published
Title: The Crystal Structure of the Human Fabp9A
Authors: Muniz, J.R.C. / Kiyani, W. / Shrestha, L. / Froese, D.S. / Krojer, T. / Vollmar, M. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / von Delft, F. / Yue, W.W.
History
DepositionOct 31, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: FATTY ACID-BINDING PROTEIN 9 TESTIS LIPID-BINDING PROTEIN, TLBP, TESTIS-TYPE FATTY ACID-BINDING PROTEIN, T-FABP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8815
Polymers17,6721
Non-polymers2094
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.486, 75.486, 113.298
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2010-

HOH

-
Components

#1: Protein FATTY ACID-BINDING PROTEIN 9 TESTIS LIPID-BINDING PROTEIN, TLBP, TESTIS-TYPE FATTY ACID-BINDING PROTEIN, T-FABP


Mass: 17672.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2 / References: UniProt: Q0Z7S8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 4.61 Å3/Da / Density % sol: 73.06 % / Description: NONE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Aug 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.53→75.49 Å / Num. obs: 49689 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 26.32 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 18.4
Reflection shellResolution: 1.53→1.61 Å / Redundancy: 6 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.53→30.6 Å / Cor.coef. Fo:Fc: 0.9678 / Cor.coef. Fo:Fc free: 0.965 / SU R Cruickshank DPI: 0.048 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.052 / SU Rfree Blow DPI: 0.052 / SU Rfree Cruickshank DPI: 0.048
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=1486. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=1486. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.1827 2517 5.07 %RANDOM
Rwork0.1686 ---
obs0.1693 49610 99.08 %-
Displacement parametersBiso mean: 31.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.4858 Å20 Å20 Å2
2---0.4858 Å20 Å2
3---0.9717 Å2
Refine analyzeLuzzati coordinate error obs: 0.186 Å
Refinement stepCycle: LAST / Resolution: 1.53→30.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 13 246 1378
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011275HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.121738HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d668SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes37HARMONIC2
X-RAY DIFFRACTIONt_gen_planes199HARMONIC5
X-RAY DIFFRACTIONt_it1275HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.97
X-RAY DIFFRACTIONt_other_torsion2.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion179SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1626SEMIHARMONIC4
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 183 5.18 %
Rwork0.241 3350 -
all0.2424 3533 -
obs--99.08 %
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)
15.15142.03742.28491.3506-0.2432.32790.02780.02610.0321-0.0086-0.03850.0229-0.0418-0.10440.0108-0.04420.0204-0.0085-0.0054-0.0176-0.04713.462223.6728-2.3424
22.0293-0.26-0.07131.75080.79322.60220.0257-0.045-0.28830.13630.05110.18540.1841-0.2005-0.07680.0007-0.0417-0.03820.01920.03240.0332-5.244413.0049-9.922
33.4806-1.5478-0.60890.16261.36883.4446-0.1291-0.4503-0.0370.0029-0.03950.0939-0.096-0.36380.1685-0.0451-0.004-0.0020.0942-0.0158-0.026-16.611324.0474-14.7997
43.2450.55711.63510.23180.06131.0759-0.01370.0237-0.04790.02330.0213-0.0637-0.02760.1153-0.0077-0.0477-0.0129-0.0146-0.001-0.0122-0.0305-2.78419.9944-18.1244
52.9871-1.10852.10220.9010.02462.6192-0.14820.09450.1167-0.04650.0123-0.0404-0.26260.1070.13590.0479-0.0414-0.04230.01760.01110.01580.116331.8842-17.8936
60.94980.281-1.2480.00971.12541.5117-0.0927-0.09920.16210.02090.02110.0818-0.12230.09150.07160.0309-0.0319-0.0737-0.042-0.0083-0.04160.481332.7729-10.2842
70.6179-0.08740.963700.54433.5656-0.021-0.12340.1459-0.051-0.04650.0714-0.228-0.15990.0675-0.00460.0016-0.0419-0.0167-0.0213-0.0624-2.953830.6341-8.3789
81.6169-1.1826-0.4942.22541.33190.70480.03-0.10530.06720.0173-0.16140.1509-0.3311-0.21980.1313-0.01040.0261-0.04570.0116-0.0243-0.0377-6.758128.84-8.2741
91.89750.4787-0.42070.58451.25152.38210.0307-0.3529-0.13150.2107-0.13020.02020.141-0.3420.0995-0.032-0.0315-0.00580.05550.0125-0.0239-6.907319.4402-4.5409
102.8107-1.6237-0.02630.8381-0.43542.53160.0965-0.32310.06730.2594-0.1113-0.0241-0.0561-0.45190.0148-0.0395-0.0126-0.03120.06910.00150.0379-9.813318.9628-7.832
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID -9:5
2X-RAY DIFFRACTION2CHAIN A AND RESID 6:15
3X-RAY DIFFRACTION3CHAIN A AND RESID 16:24
4X-RAY DIFFRACTION4CHAIN A AND RESID 25:65
5X-RAY DIFFRACTION5CHAIN A AND RESID 66:79
6X-RAY DIFFRACTION6CHAIN A AND RESID 80:88
7X-RAY DIFFRACTION7CHAIN A AND RESID 89:98
8X-RAY DIFFRACTION8CHAIN A AND RESID 99:110
9X-RAY DIFFRACTION9CHAIN A AND RESID 111:120
10X-RAY DIFFRACTION10CHAIN A AND RESID 121:131

+
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