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- PDB-1g6v: Complex of the camelid heavy-chain antibody fragment CAB-CA05 wit... -

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Basic information

Entry
Database: PDB / ID: 1g6v
TitleComplex of the camelid heavy-chain antibody fragment CAB-CA05 with bovine carbonic anhydrase
Components
  • ANTIBODY HEAVY CHAIN
  • CARBONIC ANHYDRASE
KeywordsLYASE/IMMUNE SYSTEM / antibody / antigen / complex / immunoglobulin / LYASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process ...positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / cyanamide hydratase / cyanamide hydratase activity / angiotensin-activated signaling pathway / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / one-carbon metabolic process / apical part of cell / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Carbonic anhydrase 2
Similarity search - Component
Biological speciesCamelus dromedarius (Arabian camel)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsDesmyter, A. / Decanniere, K. / Muyldermans, S. / Wyns, L.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Antigen specificity and high affinity binding provided by one single loop of a camel single-domain antibody.
Authors: Desmyter, A. / Decanniere, K. / Muyldermans, S. / Wyns, L.
History
DepositionNov 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE
K: ANTIBODY HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,8873
Polymers42,8222
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.860, 83.860, 224.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CARBONIC ANHYDRASE


Mass: 29289.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00921, carbonic anhydrase
#2: Antibody ANTIBODY HEAVY CHAIN


Mass: 13532.970 Da / Num. of mol.: 1 / Fragment: CAB-CA05, VARIABLE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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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: 4.6 Å3/Da / Density % sol: 73.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: PEG 8000, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11.7 mg/mlcAb-CA051drop
23.5 mg/mlcomplex1drop
325 %(w/v)PEG80001reservoir
40.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→26.5 Å / Num. all: 10730 / Num. obs: 10533 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 4.4
Reflection shellResolution: 3.5→3.96 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.1 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F2x, 1CA2

1f2x

1ca2


Resolution: 3.5→26.5 Å / Isotropic thermal model: grouped isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
Stereochemistry target values: Engh & Huber based CNS libraries
RfactorNum. reflectionSelection details
Rfree0.276 502 random
Rwork0.21 --
all0.21 10730 -
obs0.21 10533 -
Refinement stepCycle: LAST / Resolution: 3.5→26.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2988 0 1 0 2989
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007619
X-RAY DIFFRACTIONc_angle_deg1.35892
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 3.5 Å / Lowest resolution: 26.5 Å / σ(F): 0 / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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