[English] 日本語
Yorodumi
- PDB-3e3f: H. influenzae beta-carbonic anhydrase, variant V47A with 100 mM b... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e3f
TitleH. influenzae beta-carbonic anhydrase, variant V47A with 100 mM bicarbonate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / beta carbonic anhydrase / allosteric site mutant / Metal-binding
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 1. / Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsRowlett, R.S. / Mysliwiec, M.
CitationJournal: Biochemistry / Year: 2010
Title: Evidence for a bicarbonate "escort" site in Haemophilus influenzae beta-carbonic anhydrase .
Authors: Rowlett, R.S. / Hoffmann, K.M. / Failing, H. / Mysliwiec, M.M. / Samardzic, D.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9549
Polymers52,5182
Non-polymers4367
Water1,51384
1
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules

A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,90818
Polymers105,0364
Non-polymers87214
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11730 Å2
ΔGint-43 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.897, 83.897, 184.867
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein Carbonic anhydrase 2 / E.C.4.2.1.1 / Carbonate dehydratase 2 / beta carbonic anhydrase


Mass: 26258.932 Da / Num. of mol.: 2 / Mutation: V47A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: can, HI1301 / Plasmid: pTrc99 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P45148, 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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES, 0.7 M sodium potassium tartrate, 100 mM sodium bicarbonate, 12 mg/mL protein, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.3→76.472 Å / Num. obs: 30001 / % possible obs: 99.2 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 22.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 2.1 / Num. measured all: 16260 / Num. unique all: 4077 / Rsym value: 0.367 / % possible all: 94.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A8D

2a8d


Resolution: 2.3→28.93 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.21 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.754 / SU B: 16.172 / SU ML: 0.186 / SU R Cruickshank DPI: 0.195 / SU Rfree: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1523 5.1 %RANDOM
Rwork0.193 ---
all0.195 29926 --
obs0.195 29926 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 86.61 Å2 / Biso mean: 48.922 Å2 / Biso min: 22.53 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 22 84 3000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212973
X-RAY DIFFRACTIONr_bond_other_d0.0020.021950
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.9344030
X-RAY DIFFRACTIONr_angle_other_deg0.94134754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8395363
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.78523.869137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.63915507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7291518
X-RAY DIFFRACTIONr_chiral_restr0.0870.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02597
X-RAY DIFFRACTIONr_nbd_refined0.230.2698
X-RAY DIFFRACTIONr_nbd_other0.1980.22004
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21440
X-RAY DIFFRACTIONr_nbtor_other0.0920.21613
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2116
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0360.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2040.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2930.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.211
X-RAY DIFFRACTIONr_mcbond_it1.1321.52332
X-RAY DIFFRACTIONr_mcbond_other0.1841.5746
X-RAY DIFFRACTIONr_mcangle_it1.36322908
X-RAY DIFFRACTIONr_scbond_it2.19231334
X-RAY DIFFRACTIONr_scangle_it2.9834.51122
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 93 -
Rwork0.241 1890 -
all-1983 -
obs--90.84 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.7987-0.49860.5152.24630.96393.74260.04680.28360.1103-0.4611-0.13440.1148-0.431-0.11530.0875-0.3680.0086-0.0705-0.5066-0.01840.3827-25.317-13.612-16.786
22.89630.3152-0.38063.32811.693.87620.0667-0.27050.2239-0.2415-0.11830.309-0.6163-0.10750.0516-0.39580.00070.0015-0.5792-0.07660.4173-27.148-2.516.993
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA34 - 21534 - 215
2X-RAY DIFFRACTION2BB34 - 21634 - 216

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more