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- PDB-6rps: X-ray crystal structure of carbonic anhydrase XII complexed with ... -

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Basic information

Entry
Database: PDB / ID: 6rps
TitleX-ray crystal structure of carbonic anhydrase XII complexed with a theranostic monoclonal antibody fragment
Components
  • Carbonic anhydrase 12
  • Fab Heavy chainFragment antigen-binding
  • Fab Light chainFragment antigen-binding
KeywordsLYASE / Anticancer drugs / Carbonic Anhydrase XII / complex / monoclonal antibody
Function / homology
Function and homology information


chloride ion homeostasis / estrous cycle / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / basolateral plasma membrane / apical plasma membrane / zinc ion binding / membrane / plasma membrane
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
ACETATE ION / : / Carbonic anhydrase 12
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsAlterio, V. / Esposito, D. / De Simone, G.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Biochemical and Structural Insights into Carbonic Anhydrase XII/Fab6A10 Complex.
Authors: Alterio, V. / Kellner, M. / Esposito, D. / Liesche-Starnecker, F. / Bua, S. / Supuran, C.T. / Monti, S.M. / Zeidler, R. / De Simone, G.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 24, 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 / pdbx_struct_conn_angle / refine / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _refine.pdbx_diffrn_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 12
B: Carbonic anhydrase 12
M: Fab Light chain
N: Fab Heavy chain
L: Fab Light chain
H: Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,60917
Polymers159,6836
Non-polymers92611
Water41423
1
A: Carbonic anhydrase 12
L: Fab Light chain
H: Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,43510
Polymers79,8423
Non-polymers5937
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-106 kcal/mol
Surface area29760 Å2
MethodPISA
2
B: Carbonic anhydrase 12
M: Fab Light chain
N: Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,1757
Polymers79,8423
Non-polymers3334
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6230 Å2
ΔGint-102 kcal/mol
Surface area30010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.335, 222.165, 266.988
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Carbonic anhydrase 12 / / Carbonate dehydratase XII / Carbonic anhydrase XII / CA-XII / Tumor antigen HOM-RCC-3.1.3


Mass: 31604.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: O43570, carbonic anhydrase

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Antibody , 2 types, 4 molecules MLNH

#2: Antibody Fab Light chain / Fragment antigen-binding


Mass: 23573.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab Heavy chain / Fragment antigen-binding


Mass: 24663.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)

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Non-polymers , 6 types, 34 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#8: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.59 Å3/Da / Density % sol: 65.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.5M AMMONIUM SULFATE 0.1M SODIUM ACETATE 0.02M CADMIUM CHLORIDE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Nov 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 56400 / % possible obs: 98.1 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.044 / Rrim(I) all: 0.102 / Χ2: 0.984 / Net I/σ(I): 8.6 / Num. measured all: 272450
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.79-2.852.50.48925760.6630.3570.610.93691.8
2.85-2.92.60.42726500.7330.3050.5280.91593.1
2.9-2.962.70.38427240.8050.2710.4730.93595.5
2.96-3.022.80.34126890.8430.2390.4190.91395
3.02-3.082.80.29527770.8810.2030.360.90297.3
3.08-3.152.90.25827400.9010.1740.3130.91696.8
3.15-3.2330.22528120.9270.150.2720.87997.5
3.23-3.323.20.18627860.9510.1210.2230.91398.4
3.32-3.423.20.15127940.9670.0950.1790.89198.3
3.42-3.533.40.13328370.9780.0820.1570.90799
3.53-3.653.60.12128270.9820.0720.1420.90799.1
3.65-3.83.70.10528370.9870.0610.1220.96599.5
3.8-3.975.80.128670.9920.0440.1090.96599.7
3.97-4.187.10.08328600.9960.0330.090.97899.8
4.18-4.447.60.07128800.9980.0270.0760.986100
4.44-4.798.10.06428850.9980.0240.0681.036100
4.79-5.278.90.06729120.9980.0230.0711.05100
5.27-6.039.10.0829170.9970.0280.0851.055100
6.03-7.596.90.07829450.9960.0320.0841.077100
7.59-505.50.04430850.9980.0210.0490.92199.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WW8, 3FO0

4ww8

3fo0


Resolution: 2.79→49.65 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.889 / SU B: 11.902 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.645 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2308 1051 2 %RANDOM
Rwork0.2026 ---
obs0.2032 52250 92.4 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 116.98 Å2 / Biso mean: 36.415 Å2 / Biso min: 10.09 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0 Å2-0 Å2
2--1.71 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 2.79→49.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10790 0 25 23 10838
Biso mean--33 18.68 -
Num. residues----1386
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_mcbond_it2.2983.5375538
X-RAY DIFFRACTIONr_mcangle_it3.7255.3046906
X-RAY DIFFRACTIONr_scbond_it3.1293.6875583
LS refinement shellResolution: 2.792→2.864 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 57 -
Rwork0.349 3181 -
all-3238 -
obs--76.28 %

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