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- PDB-6rqq: X-ray crystal structure of protiated (H) large monoclinic unit ce... -

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Basic information

Entry
Database: PDB / ID: 6rqq
TitleX-ray crystal structure of protiated (H) large monoclinic unit cell CA IX SV.
ComponentsCarbonic anhydrase 9
KeywordsPROTON TRANSPORT / carbonic anhydrase / CA IX / surface variant
Function / homology
Function and homology information


Regulation of gene expression by Hypoxia-inducible Factor / response to testosterone / microvillus membrane / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane ...Regulation of gene expression by Hypoxia-inducible Factor / response to testosterone / microvillus membrane / secretion / molecular function activator activity / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / carbonic anhydrase / carbonate dehydratase activity / basolateral plasma membrane / response to hypoxia / response to xenobiotic stimulus / nucleolus / zinc ion binding / membrane / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
FORMIC ACID / Carbonic anhydrase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.276 Å
AuthorsFisher, Z. / Koruza, K.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX.
Authors: Koruza, K. / Lafumat, B. / Nyblom, M. / Mahon, B.P. / Knecht, W. / McKenna, R. / Fisher, S.Z.
History
DepositionMay 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
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_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.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.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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 9
C: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4086
Polymers56,1852
Non-polymers2234
Water12,142674
1
A: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2043
Polymers28,0931
Non-polymers1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Carbonic anhydrase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2043
Polymers28,0931
Non-polymers1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.940, 65.100, 76.290
Angle α, β, γ (deg.)90.000, 92.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 9 / Carbonate dehydratase IX / Carbonic anhydrase IX / CAIX / Membrane antigen MN / P54/58N / Renal ...Carbonate dehydratase IX / Carbonic anhydrase IX / CAIX / Membrane antigen MN / P54/58N / Renal cell carcinoma-associated antigen G250 / RCC-associated antigen G250 / pMW1


Mass: 28092.580 Da / Num. of mol.: 2 / Mutation: C174S L183S A213K A258K F259Y M350S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA9, G250, MN / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q16790, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% (w/v) PEG 4000, 0.2 M ammonium formate, 0.1 M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.27→49.5 Å / Num. obs: 122208 / % possible obs: 98.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 13.1
Reflection shellResolution: 1.27→1.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5995 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5dvx

5dvx


Resolution: 1.276→48.879 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1961 6050 4.96 %
Rwork0.1811 116012 -
obs0.1818 122062 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.71 Å2 / Biso mean: 22.8766 Å2 / Biso min: 8.65 Å2
Refinement stepCycle: final / Resolution: 1.276→48.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3960 0 8 678 4646
Biso mean--20.54 33.24 -
Num. residues----509
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074397
X-RAY DIFFRACTIONf_angle_d0.946046
X-RAY DIFFRACTIONf_chiral_restr0.089656
X-RAY DIFFRACTIONf_plane_restr0.007816
X-RAY DIFFRACTIONf_dihedral_angle_d25.2521678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.276-1.29050.35631860.30713812399897
1.2905-1.30570.32982030.30613756395997
1.3057-1.32160.29292240.28873834405897
1.3216-1.33830.2821680.27063814398297
1.3383-1.35590.26282230.26173768399197
1.3559-1.37450.24672080.25163789399798
1.3745-1.39410.28412190.24633802402197
1.3941-1.41490.27621950.23523778397397
1.4149-1.43710.24092020.22293835403798
1.4371-1.46060.22922140.22053811402598
1.4606-1.48580.2382180.21493857407598
1.4858-1.51280.20661820.20883874405698
1.5128-1.54190.20941960.19943884408099
1.5419-1.57340.20581680.20013932410099
1.5734-1.60760.20622320.19653825405799
1.6076-1.6450.21452120.18173849406199
1.645-1.68620.2131960.18043908410499
1.6862-1.73170.19682220.17373909413199
1.7317-1.78270.18811850.17183871405699
1.7827-1.84030.20642180.18243846406499
1.8403-1.9060.19112010.17433917411899
1.906-1.98230.16442150.17183866408198
1.9823-2.07260.17081730.16123913408699
2.0726-2.18180.19551610.171139824143100
2.1818-2.31850.18871960.175239574153100
2.3185-2.49750.232160.176539004116100
2.4975-2.74890.18832350.18423907414299
2.7489-3.14660.21850.176639674152100
3.1466-3.96410.16622160.15263937415399
3.9641-48.91510.16441810.16853912409396

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