[English] 日本語
Yorodumi
- PDB-3hi5: Crystal structure of Fab fragment of AL-57 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3hi5
TitleCrystal structure of Fab fragment of AL-57
Components
  • Heavy chain of Fab fragment of AL-57 against alpha L I domain
  • light chain of Fab fragment of AL-57 against alpha L I domain
KeywordsIMMUNE SYSTEM / Fab fragment / ligand mimetic / integrin / I domain / cell adhesion
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsZhang, H. / Wang, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1.
Authors: Zhang, H. / Liu, J.H. / Yang, W. / Springer, T. / Shimaoka, M. / Wang, J.H.
History
DepositionMay 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy chain of Fab fragment of AL-57 against alpha L I domain
L: light chain of Fab fragment of AL-57 against alpha L I domain


Theoretical massNumber of molelcules
Total (without water)46,7822
Polymers46,7822
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-21 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.740, 84.740, 317.170
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

-
Components

#1: Antibody Heavy chain of Fab fragment of AL-57 against alpha L I domain


Mass: 23765.510 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody light chain of Fab fragment of AL-57 against alpha L I domain


Mass: 23016.424 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 0.1M cacodylate, 0.2M Zn(Ac)2, 18% PEG8000, pH 6.4, vapor diffusion, hanging drop, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22508 / % possible obs: 92.4 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.075 / Χ2: 1.059 / Net I/σ(I): 29.091
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.596.30.36114061.005160.2
2.59-2.697.10.37917791.02175
2.69-2.829.20.35420731.072186.7
2.82-2.9612.30.31623411.047199.8
2.96-3.1514.90.23824111.0661100
3.15-3.39150.13423991.0971100
3.39-3.7314.80.0824201.0731100
3.73-4.2714.60.05924521.0431100
4.27-5.3814.20.04825011.0831100
5.38-5012.80.03627261.015199.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.4.0066refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.892 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 21.92 / SU ML: 0.236 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.5 / ESU R Free: 0.318 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1006 5.1 %RANDOM
Rwork0.234 ---
obs0.236 19789 82.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 78.91 Å2 / Biso mean: 39.342 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3271 0 0 54 3325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223362
X-RAY DIFFRACTIONr_bond_other_d0.0020.022241
X-RAY DIFFRACTIONr_angle_refined_deg1.1521.9444577
X-RAY DIFFRACTIONr_angle_other_deg0.8333.0035465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.35124.015132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.68815531
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3871514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
X-RAY DIFFRACTIONr_mcbond_it1.06552139
X-RAY DIFFRACTIONr_mcbond_other0.2835871
X-RAY DIFFRACTIONr_mcangle_it1.89753457
X-RAY DIFFRACTIONr_scbond_it3.207101223
X-RAY DIFFRACTIONr_scangle_it4.639101119
LS refinement shellResolution: 2.5→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 6 -
Rwork0.325 133 -
all-139 -
obs--8.1 %
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)
13.46362.50711.76833.7750.66693.5387-0.02450.0775-0.6151-0.00360.1758-0.21510.41010.0787-0.15130.28960.0217-0.06370.25520.01740.248334.3993-46.09036.885
21.91040.1576-0.45852.9123-0.36932.7778-0.0224-0.3153-0.12080.06670.02920.11450.1118-0.2044-0.00680.20730.01210.0080.23140.03430.231832.154-38.982416.5809
32.3598-0.1992-0.0965.31051.1665.1196-0.0568-0.57950.11460.14030.0409-0.1981-0.26210.03860.01590.25990.0244-0.02340.27520.03950.267731.4923-35.579312.1729
40.61860.87790.57031.40091.08913.49490.03260.2597-0.0425-0.20.0947-0.10340.2173-0.0633-0.12730.24280.08930.00850.2794-0.00120.333429.5946-41.3194-18.1726
51.22530.436-1.36652.13280.27945.57730.4175-0.69410.2178-0.3025-0.3303-0.6650.49561.2854-0.08720.00010.0731-0.00720.33440.00450.491137.9602-41.3866-19.5063
66.02452.8755-4.29596.9637-3.2578.24240.08370.4346-0.0485-0.05680.233-0.4568-0.0074-0.1449-0.31660.1376-0.0228-0.03370.2818-0.02670.299429.2739-38.4479-20.7548
74.82580.980.752.8903-0.04183.5559-0.03570.0046-0.5156-0.6580.0046-1.23450.6420.63560.03110.13250.18130.14450.1881-0.0550.454237.9028-45.6658-26.6483
81.7188-0.4919-0.59380.636-1.53596.0809-0.04650.02310.19390.05920.24410.3581-0.5162-0.6503-0.19760.34950.0782-0.06440.16320.02950.189924.3815-16.04431.3757
91.43471.04650.07872.6263-0.1143.27250.01220.09630.1604-0.14140.0887-0.0757-0.58510.1435-0.10090.33940.0089-0.05790.17730.02560.185832.5079-17.42747.2563
101.23260.661-1.17341.1907-0.896.1368-0.07640.04150.1339-0.11640.15660.1484-0.1613-0.3148-0.08020.29680.0431-0.05090.22160.00060.226927.4377-22.15513.6637
111.65031.69680.86826.97080.74652.678-0.05160.1325-0.2216-0.01670.1876-0.23520.130.0644-0.13610.2102-0.02120.00590.30740.00080.222623.0401-32.9378-25.4055
124.27011.08050.4082.6104-0.81310.3983-0.0176-0.0774-0.0191-0.14070.1177-0.04050.0754-0.1627-0.10020.1719-0.01210.0170.35790.00250.16813.6345-35.5969-22.6122
135.68814.58762.13336.38992.02643.24110.080.1163-0.35170.19640.0908-0.5932-0.05530.307-0.17080.17340.0108-0.00510.23440.00360.199324.1457-33.9118-21.7818
143.10632.97831.90018.62842.80264.021-0.07780.15750.0756-0.4789-0.06230.3679-0.0775-0.30850.14010.2024-0.03740.01030.38440.04030.165314.4811-32.3123-30.9957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1H2 - 22
2X-RAY DIFFRACTION2H23 - 81
3X-RAY DIFFRACTION3H82 - 108
4X-RAY DIFFRACTION4H109 - 152
5X-RAY DIFFRACTION5H153 - 168
6X-RAY DIFFRACTION6H169 - 194
7X-RAY DIFFRACTION7H195 - 220
8X-RAY DIFFRACTION8L1 - 25
9X-RAY DIFFRACTION9L26 - 81
10X-RAY DIFFRACTION10L82 - 106
11X-RAY DIFFRACTION11L107 - 146
12X-RAY DIFFRACTION12L147 - 163
13X-RAY DIFFRACTION13L164 - 185
14X-RAY DIFFRACTION14L186 - 211

+
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