[English] 日本語
Yorodumi
- PDB-2g4n: Anomalous substructure of alpha-lactalbumin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g4n
TitleAnomalous substructure of alpha-lactalbumin
ComponentsAlpha-lactalbumin
KeywordsALLERGEN / anomalous substructure of alpha-lactalbumin
Function / homology
Function and homology information


response to dehydroepiandrosterone / response to 11-deoxycorticosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / response to estradiol / lysozyme activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding ...response to dehydroepiandrosterone / response to 11-deoxycorticosterone / lactose synthase activity / lactose biosynthetic process / response to progesterone / response to estradiol / lysozyme activity / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / calcium ion binding / extracellular space / identical protein binding
Similarity search - Function
Lactalbumin / Lysozyme - #10 / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lactalbumin / Lysozyme - #10 / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Alpha-lactalbumin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsMueller-Dieckmann, C. / Weiss, M.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths.
Authors: Mueller-Dieckmann, C. / Panjikar, S. / Schmidt, A. / Mueller, S. / Kuper, J. / Geerlof, A. / Wilmanns, M. / Singh, R.K. / Tucker, P.A. / Weiss, M.S.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-lactalbumin
B: Alpha-lactalbumin
C: Alpha-lactalbumin
D: Alpha-lactalbumin
E: Alpha-lactalbumin
F: Alpha-lactalbumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,53114
Polymers85,2126
Non-polymers3198
Water1,33374
1
A: Alpha-lactalbumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2813
Polymers14,2021
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha-lactalbumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2813
Polymers14,2021
Non-polymers792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Alpha-lactalbumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Alpha-lactalbumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Alpha-lactalbumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Alpha-lactalbumin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2422
Polymers14,2021
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.430, 104.800, 119.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-208-

K

21B-207-

K

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71A
81B
91C
101D
111E
121F

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLNAA1 - 431 - 43
21GLUGLNBB1 - 431 - 43
31GLUGLNCC1 - 431 - 43
41GLUGLNDD1 - 431 - 43
51GLUGLNEE1 - 431 - 43
61GLUGLNFF1 - 431 - 43
72SERCYSAA47 - 11147 - 111
82SERCYSBB47 - 11147 - 111
92SERCYSCC47 - 11147 - 111
102SERCYSDD47 - 11147 - 111
112SERCYSEE47 - 11147 - 111
122SERCYSFF47 - 11147 - 111

-
Components

#1: Protein
Alpha-lactalbumin / Lactose synthase B protein / Allergen Bos d 4


Mass: 14202.048 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00711
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.51 Å3/Da / Density % sol: 50.91 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X12 / Wavelength: 2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 35381 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
CCP4(SCALA)data scaling
FFTphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.883 / SU B: 21.286 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.522 / ESU R Free: 0.355 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35933 722 2 %RANDOM
Rwork0.29597 ---
obs0.29731 34659 91.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.847 Å2
Baniso -1Baniso -2Baniso -3
1--1.06 Å20 Å20 Å2
2--2.82 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5856 0 8 74 5938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0226000
X-RAY DIFFRACTIONr_bond_other_d0.0120.025082
X-RAY DIFFRACTIONr_angle_refined_deg2.0531.9358142
X-RAY DIFFRACTIONr_angle_other_deg1.174311970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8345726
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25726.531294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.183151068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.394156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026624
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021110
X-RAY DIFFRACTIONr_nbd_refined0.2510.21462
X-RAY DIFFRACTIONr_nbd_other0.1880.25309
X-RAY DIFFRACTIONr_nbtor_refined0.1850.22903
X-RAY DIFFRACTIONr_nbtor_other0.0980.23202
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2183
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1520.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1970.228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.265
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.2131
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.214
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.2480.24
X-RAY DIFFRACTIONr_mcbond_it1.0311.53630
X-RAY DIFFRACTIONr_mcbond_other0.2871.51500
X-RAY DIFFRACTIONr_mcangle_it1.9392.55862
X-RAY DIFFRACTIONr_scbond_it4.98752394
X-RAY DIFFRACTIONr_scangle_it6.844102280
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A639medium positional0.170.5
2B639medium positional0.170.5
3C639medium positional0.160.5
4D639medium positional0.160.5
5E639medium positional0.210.5
6F639medium positional0.210.5
1A987loose positional0.495
2B987loose positional0.535
3C987loose positional0.525
4D987loose positional0.495
5E987loose positional0.525
6F987loose positional0.565
1A639medium thermal1.662.5
2B639medium thermal1.552.5
3C639medium thermal1.042.5
4D639medium thermal1.132.5
5E639medium thermal1.032.5
6F639medium thermal1.12.5
1A987loose thermal3.4610
2B987loose thermal3.0510
3C987loose thermal2.8610
4D987loose thermal2.7110
5E987loose thermal2.6210
6F987loose thermal2.6110
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.526 60 -
Rwork0.373 2589 -
obs--94.2 %
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)
19.10093.8805-1.64865.2728-0.88393.54440.6147-0.65391.12750.6858-0.42760.4059-0.4577-0.0765-0.1871-0.0553-0.04530.0784-0.1827-0.0968-0.056222.63051.80217.9582
28.45674.1417-2.19714.2385-0.70262.75460.8637-0.69261.08710.4117-0.59830.5185-0.19220.0502-0.2654-0.1414-0.10070.1177-0.1491-0.0929-0.02622.62171.821477.5223
34.18050.8413-0.99443.33870.43874.10980.01320.0435-0.0856-0.1279-0.0136-0.03510.2778-0.07160.0004-0.1790.01170.0047-0.2165-0.0016-0.193931.011841.15280.715
44.01920.8689-0.78863.3460.47194.15890.00060.0283-0.0879-0.10660.0015-0.03360.2599-0.0689-0.0021-0.17410.01460.0009-0.2226-0.006-0.189831.003341.130221.1526
53.1515-0.523-2.96838.65323.74377.14430.35540.32070.0753-0.4928-0.1769-0.0191-0.5064-0.362-0.1785-0.15160.03170.0242-0.1316-0.0162-0.118344.932522.371658.6802
63.3823-0.6176-2.87458.54253.76316.82390.3650.35450.0861-0.4922-0.2308-0.0207-0.4707-0.3981-0.1342-0.14710.03730.0245-0.1266-0.0122-0.125544.935622.3434118.2378
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1221 - 122
2X-RAY DIFFRACTION2BB1 - 1221 - 122
3X-RAY DIFFRACTION3CC1 - 1221 - 122
4X-RAY DIFFRACTION4DD1 - 1221 - 122
5X-RAY DIFFRACTION5EE1 - 1221 - 122
6X-RAY DIFFRACTION6FF1 - 1221 - 122

+
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://pdbjlvh1.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