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- PDB-1znc: HUMAN CARBONIC ANHYDRASE IV -

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Basic information

Entry
Database: PDB / ID: 1znc
TitleHUMAN CARBONIC ANHYDRASE IV
ComponentsCARBONIC ANHYDRASE IV
KeywordsLYASE / GPI-ANCHOR / MEMBRANE / ZINC
Function / homology
Function and homology information


bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / trans-Golgi network / brush border membrane ...bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / trans-Golgi network / brush border membrane / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / apical plasma membrane / external side of plasma membrane / perinuclear region of cytoplasm / cell surface / Golgi apparatus / extracellular exosome / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Carbonic anhydrase, CA4/CA15 / 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. ...Carbonic anhydrase, CA4/CA15 / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Carbonic anhydrase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStams, T. / Christianson, D.W.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Crystal structure of the secretory form of membrane-associated human carbonic anhydrase IV at 2.8-A resolution.
Authors: Stams, T. / Nair, S.K. / Okuyama, T. / Waheed, A. / Sly, W.S. / Christianson, D.W.
#1: Journal: Arch.Biochem.Biophys. / Year: 1996
Title: Carbonic Anhydrase Iv: Purification of a Secretory Form of the Recombinant Human Enzyme and Identification of the Positions and Importance of its Disulfide Bonds
Authors: Waheed, A. / Okuyama, T. / Heyduk, T. / Sly, W.S.
History
DepositionSep 17, 1996Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / pdbx_initial_refinement_model / software / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE IV
B: CARBONIC ANHYDRASE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0526
Polymers60,7292
Non-polymers3234
Water57632
1
A: CARBONIC ANHYDRASE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5263
Polymers30,3641
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CARBONIC ANHYDRASE IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5263
Polymers30,3641
Non-polymers1612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.500, 47.700, 141.000
Angle α, β, γ (deg.)90.00, 106.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CARBONIC ANHYDRASE IV


Mass: 30364.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HUMAN CAIV / Plasmid: PCAGGS / Cell line (production host): CHO-CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P22748, carbonic anhydrase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE RESIDUE NUMBERING IS BASED ON THE RESIDUE NUMBERING OF CARBONIC ANHYDRASE II. INSERTIONS ARE ...THE RESIDUE NUMBERING IS BASED ON THE RESIDUE NUMBERING OF CARBONIC ANHYDRASE II. INSERTIONS ARE MARKED WITH THE ADDITION OF AN ALPHABETIC CHARACTER (A, B, ...) AFTER THE RESIDUE NUMBER. DELETIONS ARE DENOTED BY MISSING RESIDUE NUMBERS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.9 %
Crystal growpH: 5.1 / Details: 25% PEG 3,350; 100MM NA ACETATE PH 5.1
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.UnitCommon nameCrystal-IDSol-ID
15-8 mg/mlprotein1drop
250 mMTris sulfate1drop
325 %PEG33501reservoir
4100 mMsodium acetate1reservoir
52 mMbenzamidine1reservoir
6mMn-octyl beta-D-glucopyranoside1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 13626 / % possible obs: 95 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.253 / % possible all: 91.8
Reflection
*PLUS
Num. measured all: 46250
Reflection shell
*PLUS
% possible obs: 91.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATA/AGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: POLYALANINE MODEL OF CAII MISSING N-TERMINAL 30

Resolution: 2.8→20 Å / Cross valid method: FREE-R / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.252 650 4.5 %
Rwork0.197 --
obs0.197 12067 85 %
Displacement parametersBiso mean: 28.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4089 0 2 34 4125
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSRms dev position: 0.2 Å
LS refinement shellResolution: 2.8→2.93 Å
RfactorNum. reflection% reflection
Rfree0.346 78 4.5 %
Rwork0.28 1261 -
obs--72.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2
LS refinement shell
*PLUS
Rfactor obs: 0.28

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