[English] 日本語
Yorodumi
- PDB-2hkf: Crystal structure of the Complex Fab M75- Peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2hkf
TitleCrystal structure of the Complex Fab M75- Peptide
Components
  • Carbonic anhydrase 9
  • Immunoglobulin Heavy chain Fab fragment
  • Immunoglobulin Light chain Fab fragment
KeywordsIMMUNE SYSTEM / Immunoglobulin / Fab fragment
Function / homology
Function and homology information


Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process ...Regulation of gene expression by Hypoxia-inducible Factor / microvillus membrane / response to testosterone / secretion / Reversible hydration of carbon dioxide / molecular function activator activity / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / nucleolus / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Immunoglobulins / Immunoglobulin-like ...Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Carbonic anhydrase 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKral, V. / Mader, P. / Stouracova, R. / Fabry, M. / Horejsi, M. / Brynda, J.
CitationJournal: Proteins / Year: 2008
Title: Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X-ray crystallography, microcalorimetry, and molecular dynamics simulations.
Authors: Kral, V. / Mader, P. / Collard, R. / Fabry, M. / Horejsi, M. / Rezacova, P. / Kozisek, M. / Zavada, J. / Sedlacek, J. / Rulisek, L. / Brynda, J.
History
DepositionJul 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Remark 999SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR IMMUNOGLOBULIN ...SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR IMMUNOGLOBULIN LIGHT CHAIN FAB FRAGMENT OR IMMUNOGLOBULIN HEAVY CHAIN FAB FRAGMENT.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
L: Immunoglobulin Light chain Fab fragment
H: Immunoglobulin Heavy chain Fab fragment
P: Carbonic anhydrase 9


Theoretical massNumber of molelcules
Total (without water)48,4743
Polymers48,4743
Non-polymers00
Water5,459303
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.388, 43.145, 58.023
Angle α, β, γ (deg.)85.03, 88.47, 85.67
Int Tables number1
Space group name H-MP1

-
Components

#1: Antibody Immunoglobulin Light chain Fab fragment


Mass: 24144.713 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma cells
#2: Antibody Immunoglobulin Heavy chain Fab fragment


Mass: 23403.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell: Hybridoma cells
#3: Protein/peptide Carbonic anhydrase 9 / Carbonic anhydrase IX / Carbonate dehydratase IX / CA-IX / CAIX / Membrane antigen MN / P54/58N / ...Carbonic anhydrase IX / Carbonate dehydratase IX / CA-IX / CAIX / Membrane antigen MN / P54/58N / Renal cell carcinoma-associated antigen G250 / RCC-associated antigen G250 / pMW1


Mass: 925.979 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
References: UniProt: Q16790, carbonic anhydrase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Tris, PEG 2000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 2, 2003
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→28.868 Å / Num. all: 57489 / Num. obs: 24418 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 12
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.191 / Mean I/σ(I) obs: 3.2 / Num. unique all: 3218 / Rsym value: 0.191 / % possible all: 87.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→28.868 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.134 / SU ML: 0.125 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24233 1243 5.1 %RANDOM
Rwork0.17563 ---
obs0.17899 23175 93.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.83 Å20.44 Å2
2---0.12 Å20.22 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.01→28.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3351 0 0 303 3654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.381.9524703
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29724.493138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75115548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7651513
X-RAY DIFFRACTIONr_chiral_restr0.1010.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022599
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.21456
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22291
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.651.52233
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05823556
X-RAY DIFFRACTIONr_scbond_it1.69931397
X-RAY DIFFRACTIONr_scangle_it2.5924.51143
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.057 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 77 -
Rwork0.2 1562 -
obs--85.41 %
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)
12.9882-1.15980.43571.6316-0.33511.12990.01170.0111-0.1075-0.0153-0.0042-0.06890.0210.059-0.0075-0.1138-0.03310.0115-0.1110.0191-0.11944.09818.2051-13.283
21.58980.3713-1.87550.8807-0.86623.44970.00760.06750.01530.14960.04840.0578-0.0034-0.1113-0.0561-0.06110-0.005-0.08740.0205-0.08348.0019-13.140616.0383
31.3608-0.8463-0.03871.1313-0.09773.071-0.0641-0.11980.09710.0860.0058-0.0471-0.1207-0.06740.0583-0.10130.0066-0.0186-0.0771-0.0123-0.0718-7.191621.54560.6657
44.6016-2.8505-0.45374.15440.5273.3234-0.2538-0.16520.18060.26970.2441-0.3879-0.08860.22280.00970.0092-0.026-0.0322-0.065-0.0199-0.00913.246-0.036123.5292
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1LA1 - 1121 - 112
2X-RAY DIFFRACTION2LA113 - 219113 - 219
3X-RAY DIFFRACTION3HB2 - 1182 - 118
4X-RAY DIFFRACTION4HB119 - 218119 - 218

+
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