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Entry
Database: PDB / ID: 6im0
TitleCrystal structure of a highly thermostable carbonic anhydrase from Persephonella marina EX-H1
ComponentsCarbonic anhydrase (Carbonate dehydratase)
KeywordsLYASE / Carbonic anhydrase / Zinc metalloenzyme / Persephonella marina EX-H1 / CO2 mineralization / CO2 capture and storage
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / 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, prokaryotic-like / 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
BICARBONATE ION / Carbonic anhydrase
Similarity search - Component
Biological speciesPersephonella marina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJin, M.S. / Kim, S. / Sung, J. / Yeon, J. / Choi, S.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B4003278 Korea, Republic Of
CitationJournal: Mol.Cells / Year: 2019
Title: Crystal Structure of a Highly Thermostable alpha-Carbonic Anhydrase from Persephonella marina EX-H1.
Authors: Kim, S. / Sung, J. / Yeon, J. / Choi, S.H. / Jin, M.S.
History
DepositionOct 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 31, 2019Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_asym.entity_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.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_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id / _struct_site_gen.symmetry
Revision 2.1Nov 22, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase (Carbonate dehydratase)
B: Carbonic anhydrase (Carbonate dehydratase)
C: Carbonic anhydrase (Carbonate dehydratase)
D: Carbonic anhydrase (Carbonate dehydratase)
E: Carbonic anhydrase (Carbonate dehydratase)
F: Carbonic anhydrase (Carbonate dehydratase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,67438
Polymers166,3436
Non-polymers2,33132
Water4,486249
1
A: Carbonic anhydrase (Carbonate dehydratase)
C: Carbonic anhydrase (Carbonate dehydratase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,29013
Polymers55,4482
Non-polymers84211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-125 kcal/mol
Surface area20570 Å2
MethodPISA
2
B: Carbonic anhydrase (Carbonate dehydratase)
hetero molecules

E: Carbonic anhydrase (Carbonate dehydratase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,29013
Polymers55,4482
Non-polymers84211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area1950 Å2
ΔGint-126 kcal/mol
Surface area20530 Å2
MethodPISA
3
D: Carbonic anhydrase (Carbonate dehydratase)
hetero molecules

F: Carbonic anhydrase (Carbonate dehydratase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,09512
Polymers55,4482
Non-polymers64710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area2460 Å2
ΔGint-121 kcal/mol
Surface area20470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.885, 109.034, 123.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 22 - 243 / Label seq-ID: 22 - 243

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14AA
24EE
15AA
25FF
16BB
26CC
17BB
27DD
18BB
28EE
19BB
29FF
110CC
210DD
111CC
211EE
112CC
212FF
113DD
213EE
114DD
214FF
115EE
215FF

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Carbonic anhydrase (Carbonate dehydratase)


Mass: 27723.904 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Persephonella marina (strain DSM 14350 / EX-H1) (bacteria)
Strain: DSM 14350 / EX-H1 / Gene: PERMA_1443 / Production host: Escherichia coli (E. coli) / References: UniProt: C0QRB5, carbonic anhydrase

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Non-polymers , 5 types, 281 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM sodium HEPES pH 7.5, 28-32% (w/v) polyethylene glycol (PEG) 400, and 200-400 mM calcium chloride dehydrate.

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→123.19 Å / Num. obs: 47255 / % possible obs: 97.9 % / Redundancy: 3.4 % / CC1/2: 0.955 / Rpim(I) all: 0.083 / Net I/σ(I): 9.8
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 4968 / CC1/2: 0.758 / Rpim(I) all: 0.318

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EKI

6eki


Resolution: 2.6→123.19 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / SU B: 12.018 / SU ML: 0.24 / Cross valid method: THROUGHOUT / ESU R: 1.06 / ESU R Free: 0.294 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22719 2478 5 %RANDOM
Rwork0.18993 ---
obs0.19183 47255 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.941 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0 Å20.62 Å2
2--3.63 Å20 Å2
3----2.74 Å2
Refinement stepCycle: 1 / Resolution: 2.6→123.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10818 0 110 249 11177
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911220
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210657
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.95315073
X-RAY DIFFRACTIONr_angle_other_deg1.103324709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56951326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37224.333540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.888152040
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.861554
X-RAY DIFFRACTIONr_chiral_restr0.0850.21512
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112438
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022514
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0264.0685322
X-RAY DIFFRACTIONr_mcbond_other3.0264.0685321
X-RAY DIFFRACTIONr_mcangle_it4.7046.0986642
X-RAY DIFFRACTIONr_mcangle_other4.7046.0986643
X-RAY DIFFRACTIONr_scbond_it4.1344.5665898
X-RAY DIFFRACTIONr_scbond_other4.1334.5665898
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6256.6198432
X-RAY DIFFRACTIONr_long_range_B_refined8.48431.42411814
X-RAY DIFFRACTIONr_long_range_B_other8.48631.43411793
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A285880.01
12B285880.01
21A285060.03
22C285060.03
31A284880.03
32D284880.03
41A285360.02
42E285360.02
51A285000.03
52F285000.03
61B285140.02
62C285140.02
71B284980.02
72D284980.02
81B285440.01
82E285440.01
91B285040.02
92F285040.02
101C284480.03
102D284480.03
111C285040.03
112E285040.03
121C284520.03
122F284520.03
131D284700.03
132E284700.03
141D284740.03
142F284740.03
151E284760.03
152F284760.03
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 192 -
Rwork0.295 3333 -
obs--93.75 %

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