[English] 日本語
Yorodumi
- PDB-4mfg: 2.0 Angstrom Resolution Crystal Structure of Putative Carbonic An... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mfg
Title2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.
ComponentsPutative acyltransferase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Single-stranded left-handed beta-helix / gamma-carbonic anhydrase-like
Function / homology
Function and homology information


acyltransferase activity / metal ion binding
Similarity search - Function
Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Putative acyltransferase
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMinasov, G. / Wawrzak, Z. / Kudritska, M. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.0 Angstrom Resolution Crystal Structure of Putative Carbonic Anhydrase from Clostridium difficile.
Authors: Minasov, G. / Wawrzak, Z. / Kudritska, M. / Grimshaw, S. / Kwon, K. / Savchenko, A. / Anderson, W.F.
History
DepositionAug 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 20, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.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_alt_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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative acyltransferase
B: Putative acyltransferase
C: Putative acyltransferase
D: Putative acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,69010
Polymers73,4074
Non-polymers2836
Water7,314406
1
A: Putative acyltransferase
B: Putative acyltransferase
C: Putative acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2557
Polymers55,0553
Non-polymers2004
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-53 kcal/mol
Surface area20700 Å2
MethodPISA
2
D: Putative acyltransferase
hetero molecules

D: Putative acyltransferase
hetero molecules

D: Putative acyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3049
Polymers55,0553
Non-polymers2496
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area4730 Å2
ΔGint-53 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.089, 127.089, 76.732
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11D-201-

MG

21A-405-

HOH

31D-385-

HOH

-
Components

#1: Protein
Putative acyltransferase / Putative Carbonic Anhydrase


Mass: 18351.639 Da / Num. of mol.: 4 / Fragment: Putative Carbonic Anhydrase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD630_27480 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q183I2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein: 2.7mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 12.5mM Suberic acid, 12.5mM Sebcic acid, 12.5mM Hexadecanedioic acid, 12.5mM Dodecanedioic acid, 40% Ethanol, 0.1M Hepes pH ...Details: Protein: 2.7mg/mL, 0.3M Sodium cloride, 0.1M HEPES pH 7.5; Screen: 12.5mM Suberic acid, 12.5mM Sebcic acid, 12.5mM Hexadecanedioic acid, 12.5mM Dodecanedioic acid, 40% Ethanol, 0.1M Hepes pH 7.5, 2% MPD, 20% (w/v) PEG 3350; Cryo: paratone., VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 47926 / Num. obs: 47926 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 29.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2398 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.8.0046refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XHD

1xhd


Resolution: 2→29.36 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 12 / SU ML: 0.168
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26663 2416 5.1 %RANDOM
Rwork0.21158 ---
all0.21439 45299 --
obs0.21439 45299 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.179 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.45 Å20 Å2
2--0.89 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2→29.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5152 0 6 406 5564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195400
X-RAY DIFFRACTIONr_bond_other_d0.0010.025135
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.9627309
X-RAY DIFFRACTIONr_angle_other_deg0.785311894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7625698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.4426.271236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97115963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2291516
X-RAY DIFFRACTIONr_chiral_restr0.1020.2833
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.026204
X-RAY DIFFRACTIONr_gen_planes_other0.0170.021104
X-RAY DIFFRACTIONr_mcbond_it1.5061.7172759
X-RAY DIFFRACTIONr_mcbond_other1.5051.7162758
X-RAY DIFFRACTIONr_mcangle_it2.1992.5623468
X-RAY DIFFRACTIONr_mcangle_other2.1982.5633469
X-RAY DIFFRACTIONr_scbond_it2.4122.0122639
X-RAY DIFFRACTIONr_scbond_other2.3972.0092633
X-RAY DIFFRACTIONr_scangle_other3.3222.9163841
X-RAY DIFFRACTIONr_long_range_B_refined6.83815.3096560
X-RAY DIFFRACTIONr_long_range_B_other6.62814.8186410
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 192 -
Rwork0.296 3323 -
obs-3323 100 %
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)
114.8316-0.6283-3.87174.4935-3.36025.9467-0.35160.5824-0.1109-0.03170.2765-0.00480.37420.28780.0750.13360.12490.02310.3503-0.01930.0313-57.141429.065315.1269
26.317-1.0078-2.1563.7081-2.11893.93360.053-0.23030.00220.2761-0.08440.22350.066-0.74550.03140.3493-0.05850.03770.6454-0.110.1289-46.269417.148712.4188
31.5461-0.3392-0.04021.75490.44574.76060.04310.0572-0.08580.2395-0.13390.21980.2099-1.03650.09080.12680.01650.03660.318-0.02410.0416-45.005917.22584.3079
41.82530.298-0.70351.7026-0.33535.0049-0.08550.1339-0.0994-0.01390.02920.0850.5463-1.26910.05630.158-0.0563-0.01170.4034-0.04960.0578-45.660813.9631-10.3596
50.8074-0.642.25494.2536-5.533527.0209-0.0213-0.0244-0.0902-0.248-0.2025-0.09590.8015-0.59960.22380.2362-0.15080.06740.1516-0.04430.0807-47.33740.264-5.967
66.2043-6.16112.73417.2129-7.470421.929-0.4377-0.92670.2230.27010.9297-0.0710.6368-0.441-0.49210.3917-0.09370.01110.2484-0.01390.0892-42.61741.8079.815
78.05132.9779-1.9855.9674-0.948711.8866-0.28390.28010.0678-0.76330.1703-0.08940.2205-1.10030.11360.1724-0.0831-0.02120.2609-0.04820.0569-9.350335.519914.9881
83.7485-0.74021.17045.78783.39772.7638-0.0794-0.53610.66830.073-0.25060.0816-0.1767-0.28620.330.6933-0.15220.01930.504-0.07350.1434-27.160734.266714.1032
91.1180.08920.49531.0435-0.23944.5506-0.1893-0.02910.18960.0140.0096-0.0732-1.2810.44710.17980.368-0.1313-0.05420.1612-0.01170.0579-26.155532.10292.0412
104.44850.20250.82581.54430.45274.1776-0.26870.29080.0593-0.2650.09980.0481-1.16130.46840.16890.3478-0.1299-0.05780.14490.01890.0318-26.623131.0841-10.9175
112.5368-0.759-1.59524.76420.71047.25230.09240.0084-0.0484-0.8193-0.1020.1003-1.832-0.22160.00960.6860.0325-0.10050.21450.04770.1343-32.87237.3016-16.4713
122.92820.8037-1.86081.4467-2.93416.5053-0.3214-0.54590.16650.7070.10970.05-1.8868-0.4640.21181.18930.4573-0.19930.5119-0.18040.396-40.241638.26814.8154
132.50462.502-0.33318.6771-2.30050.7020.20170.1962-0.41010.0497-0.2323-0.21860.05970.15070.03060.56410.0499-0.02340.34480.06410.1305-24.9726-4.172214.8214
142.652-0.03920.33341.2683-0.39535.0456-0.0354-0.1997-0.15870.0653-0.1238-0.14490.88210.81330.15920.26280.09480.01730.24380.07070.0379-23.34438.29236.272
151.54280.5069-0.32953.3727-1.1816.156-0.0472-0.0877-0.0708-0.2251-0.1393-0.09031.01541.07210.18650.22720.17030.05070.21870.0480.0252-21.7288.2701-6.9277
1629.06639.69832.50768.72385.91755.28880.20320.5817-0.59750.0585-0.0392-0.34840.45950.1297-0.1640.57770.33070.00370.2980.05560.0547-19.11073.732-16.3743
179.4586-0.10023.51661.21930.11285.8582-0.1370.30040.0764-0.2694-0.03820.12090.48051.53440.17520.29070.14630.09880.59540.08510.131-13.451613.2823-15.6312
181.05930.43321.23544.4284.728819.26920.0328-0.00060.20360.6623-0.2717-0.53660.76940.97030.2390.15540.0117-0.06180.57870.0730.1709-10.053716.85016.5845
198.18453.11332.58897.8354-0.36213.2963-0.18930.8546-0.1125-0.00080.0308-0.2532-0.9941-0.27410.15850.20290.084-0.05120.2542-0.00590.0285-36.236226.9425-23.0708
200.6817-0.11270.4411.7294-0.02452.8138-0.0324-0.04650.04730.2323-0.0878-0.226-0.18590.87880.12030.1858-0.0252-0.05280.35310.03530.0828-49.548839.4802-32.3828
215.50573.35362.62258.6981.67062.67860.0803-0.3378-0.0249-0.141-0.2779-0.4288-0.24190.95150.19760.2807-0.1478-0.02460.92110.13950.1464-47.784840.8913-43.7
221.3896-0.5915-0.80811.36190.10783.26850.05550.04820.1158-0.0446-0.0816-0.05-0.27590.81870.02610.119-0.0395-0.00360.27310.0470.0691-50.288741.0519-51.9227
232.4011.8404-5.11772.5539-0.409923.3765-0.0991-0.2446-0.0117-0.0301-0.2820.0343-0.29030.79670.38110.2563-0.193-0.06740.23050.08380.1234-48.284456.2719-47.4272
249.3341-6.2576-9.06244.73384.937511.4225-0.4896-0.77110.07270.53930.4584-0.01950.19920.91240.03120.467-0.0750.02160.18640.00260.1768-53.319354.1904-28.3701
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 8
2X-RAY DIFFRACTION2A9 - 29
3X-RAY DIFFRACTION3A30 - 68
4X-RAY DIFFRACTION4A69 - 144
5X-RAY DIFFRACTION5A145 - 154
6X-RAY DIFFRACTION6A155 - 165
7X-RAY DIFFRACTION7B-2 - 8
8X-RAY DIFFRACTION8B9 - 20
9X-RAY DIFFRACTION9B21 - 94
10X-RAY DIFFRACTION10B95 - 122
11X-RAY DIFFRACTION11B123 - 147
12X-RAY DIFFRACTION12B148 - 165
13X-RAY DIFFRACTION13C-3 - 15
14X-RAY DIFFRACTION14C16 - 67
15X-RAY DIFFRACTION15C68 - 121
16X-RAY DIFFRACTION16C122 - 128
17X-RAY DIFFRACTION17C129 - 149
18X-RAY DIFFRACTION18C150 - 165
19X-RAY DIFFRACTION19D-3 - 6
20X-RAY DIFFRACTION20D7 - 81
21X-RAY DIFFRACTION21D82 - 94
22X-RAY DIFFRACTION22D95 - 139
23X-RAY DIFFRACTION23D140 - 154
24X-RAY DIFFRACTION24D155 - 165

+
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://pdbjlvh1.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