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- PDB-3mc2: Crystal Structure of the Murine Inhibitor of Carbonic Anhydrase -

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Basic information

Entry
Database: PDB / ID: 3mc2
TitleCrystal Structure of the Murine Inhibitor of Carbonic Anhydrase
ComponentsInhibitor of Carbonic Anhydrase
KeywordsLYASE INHIBITOR / mICA / Transferrin Superfamily
Function / homology
Function and homology information


enzyme inhibitor activity / extracellular space
Similarity search - Function
Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Inhibitor of carbonic anhydrase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsEckenroth, B.E. / Mason, A.B. / Everse, S.J.
CitationJournal: Protein Sci. / Year: 2010
Title: The structure and evolution of the murine inhibitor of carbonic anhydrase: A member of the transferrin superfamily.
Authors: Eckenroth, B.E. / Mason, A.B. / McDevitt, M.E. / Lambert, L.A. / Everse, S.J.
History
DepositionMar 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type
Revision 1.4Oct 6, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inhibitor of Carbonic Anhydrase
B: Inhibitor of Carbonic Anhydrase
C: Inhibitor of Carbonic Anhydrase
D: Inhibitor of Carbonic Anhydrase


Theoretical massNumber of molelcules
Total (without water)302,8804
Polymers302,8804
Non-polymers00
Water00
1
A: Inhibitor of Carbonic Anhydrase


Theoretical massNumber of molelcules
Total (without water)75,7201
Polymers75,7201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Inhibitor of Carbonic Anhydrase


Theoretical massNumber of molelcules
Total (without water)75,7201
Polymers75,7201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Inhibitor of Carbonic Anhydrase


Theoretical massNumber of molelcules
Total (without water)75,7201
Polymers75,7201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Inhibitor of Carbonic Anhydrase


Theoretical massNumber of molelcules
Total (without water)75,7201
Polymers75,7201
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.559, 136.928, 155.575
Angle α, β, γ (deg.)90.000, 90.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A,B, using restrain
22chain C,D, using restrain

NCS ensembles :
ID
1
2

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Components

#1: Protein
Inhibitor of Carbonic Anhydrase


Mass: 75719.906 Da / Num. of mol.: 4 / Fragment: Residues 20-700 / Mutation: N489D, N664D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: C57BL/10J / Gene: 1300017J02Rik, mICA / Plasmid: pNUT / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / Tissue (production host): Kidney / References: UniProt: Q9DBD0
Has protein modificationY

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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: 2.44 Å3/Da / Density % sol: 49.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12% PEG 3350, pH 7.5, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 104 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 6, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.4→19 Å / Num. obs: 105646 / % possible obs: 94.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 20.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 3.2 / % possible all: 71.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_RNP

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Processing

Software
NameVersionClassificationNB
CNSrefinement
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19 Å / Occupancy max: 1 / Occupancy min: 0 / σ(F): 1304
RfactorNum. reflection% reflection
Rfree0.301 10093 9 %
Rwork0.239 94188 -
obs-104281 93.2 %
Solvent computationBsol: 43.648 Å2
Displacement parametersBiso max: 134.94 Å2 / Biso mean: 75.37 Å2 / Biso min: 1.87 Å2
Baniso -1Baniso -2Baniso -3
1--25.042 Å20 Å20.756 Å2
2--30.332 Å20 Å2
3----5.29 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20772 0 0 0 20772
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.408
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11BX-RAY DIFFRACTION0.113restrain200
22DX-RAY DIFFRACTION0.106restrain200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.510.4019630.40186299592
2.51-2.640.38411720.3771123812410
2.64-2.810.37313100.3531219113501
2.81-3.020.36113480.3351232413672
3.02-3.320.34713220.2981245513777
3.32-3.80.30813070.2491253813845
3.8-4.780.26713460.1841251713863
4.78-190.2613250.1791229613621
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param

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