[English] 日本語
Yorodumi
- PDB-7rlr: Crystal Structure of K83A Mutant of Class D beta-lactamase from C... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rlr
TitleCrystal Structure of K83A Mutant of Class D beta-lactamase from Clostridium difficile 630
ComponentsBeta-lactamase
KeywordsHYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / blaD
Function / homology
Function and homology information


penicillin binding / antibiotic catabolic process / cell wall organization / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-D active site / Beta-lactamase class-D active site. / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
ACETATE ION / Beta-lactamase
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Rosas-Lemus, M. / Jedrzejczak, R. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of K83A Mutant of Class D beta-lactamase from Clostridium difficile 630
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Rosas-Lemus, M. / Jedrzejczak, R. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: Beta-lactamase
B: Beta-lactamase
C: Beta-lactamase
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,45918
Polymers116,8404
Non-polymers61914
Water15,385854
1
A: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3404
Polymers29,2101
Non-polymers1303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4295
Polymers29,2101
Non-polymers2194
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3043
Polymers29,2101
Non-polymers942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-lactamase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3866
Polymers29,2101
Non-polymers1765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.534, 93.621, 138.067
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Beta-lactamase


Mass: 29209.986 Da / Num. of mol.: 4 / Mutation: K83A
Source method: isolated from a genetically manipulated source
Details: Class D beta-lactamase / Source: (gene. exp.) Clostridioides difficile (bacteria) / Strain: 630 / Gene: CD630_04580 / Plasmid: pMCSG104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 Magic / References: UniProt: Q188Q3, beta-lactamase

-
Non-polymers , 5 types, 868 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.5 mg/ml, 0.01M Tris pH 8.3, 5mM DDT; Screen: PEGSs II (D1), 0.1M Sodium acetate, 0.1M HEPES pH 7.5, 22% (w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2020 / Details: Be
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 90491 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.028 / Rrim(I) all: 0.074 / Rsym value: 0.068 / Χ2: 1.008 / Net I/σ(I): 26.7
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 7 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4507 / CC1/2: 0.779 / CC star: 0.936 / Rpim(I) all: 0.321 / Rrim(I) all: 0.853 / Rsym value: 0.79 / Χ2: 1.006 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UE2
Resolution: 1.88→29.71 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.55 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1978 4441 4.9 %RANDOM
Rwork0.1684 ---
obs0.1699 85969 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.67 Å2 / Biso mean: 33.134 Å2 / Biso min: 14.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0 Å2
2---1.25 Å20 Å2
3---0.81 Å2
Refinement stepCycle: final / Resolution: 1.88→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8114 0 33 886 9033
Biso mean--39.75 36.73 -
Num. residues----1006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0138460
X-RAY DIFFRACTIONr_bond_other_d0.0010.0187758
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.6411397
X-RAY DIFFRACTIONr_angle_other_deg0.3451.5918149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.69851037
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.76425.057437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.754151607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.711523
X-RAY DIFFRACTIONr_chiral_restr0.0620.21085
X-RAY DIFFRACTIONr_gen_planes_refined0.0550.029489
X-RAY DIFFRACTIONr_gen_planes_other0.0510.021696
LS refinement shellResolution: 1.881→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 317 -
Rwork0.228 6132 -
all-6449 -
obs--97.88 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.19810.5563-0.2862.3877-0.40392.92140.07240.15740.0075-0.11210.0037-0.1605-0.11360.2635-0.07610.02010.0120.01920.1671-0.00210.05826.9632-19.8125-1.7635
21.1902-0.3402-0.36811.31250.2420.99140.06690.02430.17750.0104-0.0240.0299-0.096-0.1273-0.04290.03530.01040.00780.12440.00330.0325-19.5603-15.29510.3725
31.10710.2562-0.05761.7095-0.37721.32190.06460.02520.0483-0.0242-0.0252-0.0116-0.0033-0.0614-0.03950.02720.00570.00330.1207-0.00470.0045-12.879-20.679-2.2417
46.42630.67075.22632.34610.87847.5906-0.14160.26210.5904-0.10020.0339-0.2331-0.51120.21190.10770.0573-0.00970.03620.02760.02350.1254-7.9854-3.0121-2.9244
51.87450.5125-0.12833.3421-1.62942.48710.05540.03820.24850.0234-0.0564-0.0877-0.12640.12780.0010.0104-0.00030.00960.0805-0.01520.0482-2.3142-15.64792.3414
61.96140.6572-1.18752.8908-0.82462.15960.1255-0.11050.12240.2542-0.0281-0.1103-0.1350.1132-0.09740.056-0.011-0.03120.1154-0.02980.04862.1739-15.75628.8945
76.9893.8697-0.61536.5145-1.04392.2946-0.02380.3771-0.2399-0.68370.1192-0.15650.32220.2142-0.09550.18010.07920.04490.1149-0.03770.14776.2166-46.0563-41.3926
80.4376-0.14350.14835.64871.79062.39740.0343-0.0738-0.20860.0592-0.0184-0.26210.26740.1269-0.01590.10810.0803-0.01060.10620.01330.17666.1441-48.6371-32.5478
91.526-0.4870.23070.9787-0.14221.36490.0035-0.02320.02550.0287-0.0067-0.0113-0.0244-0.03670.00320.0480.01130.01780.0499-0.00870.0134-9.1638-26.9932-28.6305
101.7255-0.43520.08641.71650.25251.54990.07840.0816-0.1822-0.1509-0.06950.07780.110.0372-0.00890.06320.02950.00290.0273-0.01060.0301-5.7206-35.4399-33.3329
1111.27297.59617.40656.8574.48345.30950.13860.2341-0.4866-0.07240.0522-0.48030.21790.2659-0.19080.04990.05740.01130.0792-0.0170.09214.2379-36.7333-35.7174
123.85680.14731.19373.56970.36452.20120.09920.5076-0.1799-0.6213-0.0804-0.35010.05370.3991-0.01880.1610.07650.06950.1444-0.01420.07174.7208-38.6794-43.004
134.62391.5755-0.47174.043-0.53072.56980.12460.08040.78350.01260.02080.4149-0.1734-0.2877-0.14530.12380.10950.07470.12110.12090.3905-46.45317.0437-36.619
142.6079-0.8187-0.59031.54110.19520.7360.12490.3145-0.0092-0.1328-0.0780.11130.0359-0.1237-0.04690.07080.02950.00920.11780.02190.0243-33.35-17.3217-34.4992
152.4612-0.7812-0.0461.5697-0.59231.34280.12770.02980.1237-0.0309-0.0250.0906-0.022-0.1169-0.10270.05840.0220.05280.07120.02230.0596-42.8967-13.4154-25.1006
161.26990.6871-0.53682.738-1.40712.06380.08440.17580.3832-0.01070.0250.0227-0.19280.0956-0.10940.0830.03270.06510.08480.06190.1675-28.4896-1.5226-34.0851
173.71731.6244-0.28283.196-0.72932.12570.05150.51120.5603-0.35950.07260.3178-0.0562-0.2731-0.12410.09290.08260.03260.1720.14470.1697-44.0815-2.2796-41.0587
182.1323-1.53280.30482.6208-2.625212.25010.0147-0.1148-0.20990.09930.19830.35460.14660.3804-0.2130.05040.00470.03050.09420.04360.0704-30.64415.5328-49.7552
192.9957-0.30140.5357.4187-0.17143.4854-0.06080.090.08840.0869-0.23050.37480.4951-0.62740.29130.1022-0.12990.09020.1673-0.11490.166-15.1846-66.1606-8.6891
201.83050.7995-0.13281.94770.94691.9966-0.0562-0.1454-0.21740.4171-0.1428-0.14720.131-0.09920.19890.1978-0.038-0.02350.05820.0230.07713.3884-52.38354.3875
217.7416-2.9328-4.16312.171-1.17613.8274-0.2678-0.8307-0.4440.6282-0.0910.03390.20620.27560.35880.4234-0.0506-0.05050.19170.03710.07044.1092-60.854918.4735
221.02610.02950.4761.46570.50692.9296-0.04640.0224-0.07160.2404-0.22360.13370.2432-0.27060.270.0841-0.0620.05270.0591-0.04910.0484-3.2557-56.1898-3.061
230.69190.22250.33680.5755-0.28584.88960.0208-0.0129-0.23820.1812-0.20490.10770.7003-0.22630.18420.2626-0.11770.1290.1407-0.08430.2307-5.6147-66.9343-8.1505
245.2634-0.25820.880910.33964.25021.9381-0.1712-0.27260.40660.18880.07660.06880.0556-0.03570.09460.0842-0.00090.00940.06830.0180.0764-5.5001-66.3029-29.8603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A40 - 72
2X-RAY DIFFRACTION2A73 - 164
3X-RAY DIFFRACTION3A165 - 204
4X-RAY DIFFRACTION4A205 - 222
5X-RAY DIFFRACTION5A223 - 260
6X-RAY DIFFRACTION6A261 - 287
7X-RAY DIFFRACTION7B41 - 60
8X-RAY DIFFRACTION8B61 - 75
9X-RAY DIFFRACTION9B76 - 164
10X-RAY DIFFRACTION10B165 - 234
11X-RAY DIFFRACTION11B235 - 253
12X-RAY DIFFRACTION12B254 - 288
13X-RAY DIFFRACTION13C41 - 73
14X-RAY DIFFRACTION14C74 - 138
15X-RAY DIFFRACTION15C139 - 192
16X-RAY DIFFRACTION16C193 - 227
17X-RAY DIFFRACTION17C228 - 286
18X-RAY DIFFRACTION18C287 - 294
19X-RAY DIFFRACTION19D41 - 71
20X-RAY DIFFRACTION20D72 - 162
21X-RAY DIFFRACTION21D163 - 172
22X-RAY DIFFRACTION22D173 - 239
23X-RAY DIFFRACTION23D240 - 288
24X-RAY DIFFRACTION24D289 - 294

+
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