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- PDB-1mqk: Crystal structure of the unliganded Fv-fragment of the anti-cytoc... -

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Basic information

Entry
Database: PDB / ID: 1mqk
TitleCrystal structure of the unliganded Fv-fragment of the anti-cytochrome C oxidase antibody 7E2
Components
  • antibody 7E2 FV fragment, heavy chain
  • antibody 7E2 FV fragment, light chain
KeywordsIMMUNE SYSTEM / antibody / membrane protein / cytochrome C oxidase / high-resolution structure
Function / homology
Function and homology information


immunoglobulin complex / immunoglobulin mediated immune response / antigen binding / adaptive immune response / blood microparticle / immune response / extracellular space
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Ig kappa chain V-V region MOPC 149 / Ig heavy chain V region 5-84
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
AuthorsEssen, L.-O. / Harrenga, A. / Ostermeier, C. / Michel, H.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: 1.3 A X-ray structure of an antibody Fv fragment used for induced membrane-protein crystallization.
Authors: Essen, L.O. / Harrenga, A. / Ostermeier, C. / Michel, H.
#1: Journal: Proteins / Year: 1995
Title: Crystals of an antibody Fv fragment against an integral membrane protein diffracting to 1.28 resolution
Authors: Ostermeier, C. / Essen, L.-O. / Michel, H.
#2: Journal: Nat.Struct.Biol. / Year: 1995
Title: Fv fragment-mediated crystallization of the membrane protein bacterial cytochrome C oxidase
Authors: Ostermeier, C. / Iwata, S. / Ludwig, B. / Michel, H.
#3: Journal: Nature / Year: 1995
Title: Structure at 2.8 resolution of cytochrome C oxidase from Paracoccus denitrificans
Authors: Iwata, S. / Ostermeier, C. / Ludwig, B. / Michel, H.
#4: Journal: J.Biol.Chem. / Year: 1999
Title: The cytochrome C oxidase from Paracoccus denitrificans does not change the metal center upon reduction
Authors: Harrenga, A. / Michel, H.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: Structure at 2.7 resolution of the Paracoccus denitrificans two-subunit cytochrome C oxidase complexed with an antibody Fv fragment
Authors: Ostermeier, C. / Harrenga, A. / Ermler, U. / Michel, H.
History
DepositionSep 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Remark 999SEQUENCE ACCORDING TO THE AUTHOR, THE SEQUENCE FOR THE HEAVY AND LIGHT CHAINS OF ANTIBODY 7E2 HAS ...SEQUENCE ACCORDING TO THE AUTHOR, THE SEQUENCE FOR THE HEAVY AND LIGHT CHAINS OF ANTIBODY 7E2 HAS NOT BEEN DEPOSITED IN ANY SEQUENCE DATABASE. SOME SEQUENCE INFORMATION IS PRESENT IN PDB ENTRY 1QLE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: antibody 7E2 FV fragment, light chain
H: antibody 7E2 FV fragment, heavy chain


Theoretical massNumber of molelcules
Total (without water)27,5862
Polymers27,5862
Non-polymers00
Water5,729318
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-16 kcal/mol
Surface area11280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.436, 56.045, 99.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody antibody 7E2 FV fragment, light chain


Mass: 13260.795 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P01636
#2: Antibody antibody 7E2 FV fragment, heavy chain


Mass: 14324.923 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pASK68 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P18525
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 277 K / Method: microdialysis / pH: 6
Details: sodium phosphate, pH 6.0, MICRODIALYSIS, temperature 277K
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein11
2100 mMsodium phosphate11pH6.0

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 12, 1993 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→22.5 Å / Num. obs: 64251 / % possible obs: 85.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.8 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.4 / Net I/σ(I): 28.6
Reflection shellResolution: 1.28→1.31 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.218 / Mean I/σ(I) obs: 5.2 / % possible all: 63.4
Reflection
*PLUS
Num. measured all: 178789 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 63.4 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
X-PLORmodel building
SHELXLrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLE

1qle


Resolution: 1.28→8 Å / Isotropic thermal model: anisotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used weighted full matrix least squares procedure of SHELX-93 to generate model. Only isotropic model provided
RfactorNum. reflectionSelection details
Rfree0.196 1922 random
Rwork0.136 --
all0.136 64005 -
obs0.136 64005 -
Displacement parametersBiso mean: 22.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å / Luzzati sigma a obs: 0.07 Å
Refinement stepCycle: LAST / Resolution: 1.28→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 0 318 2193
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d2.28
X-RAY DIFFRACTIONs_bond_d0.021
X-RAY DIFFRACTIONo_dihedral_angle_d28.1
Software
*PLUS
Name: SHELXL / Version: 93 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / % reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.28
X-RAY DIFFRACTIONs_dihedral_angle_d
X-RAY DIFFRACTIONs_dihedral_angle_deg28.1

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