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- PDB-5kkf: Crystal structure of TEM1 beta-lactamase mutant I263L -

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Basic information

Entry
Database: PDB / ID: 5kkf
TitleCrystal structure of TEM1 beta-lactamase mutant I263L
ComponentsBeta-lactamase TEM
KeywordsHYDROLASE
Function / homology
Function and homology information


beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic
Similarity search - Function
Beta-lactamase, class-A active site / Beta-lactamase class-A active site. / Beta-lactamase class A, catalytic domain / Beta-lactamase enzyme family / Beta-lactamase, class-A / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Beta-lactamase/transpeptidase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.82 Å
AuthorsRoose, B.W. / Dmochowski, I.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM097478 United States
Department of Defense Lung Cancer Research ProgramW81XWH-14-1-0424 United States
CitationJournal: Chemphyschem / Year: 2018
Title: A Structural Basis for129Xe Hyper-CEST Signal in TEM-1 beta-Lactamase.
Authors: Roose, B.W. / Zemerov, S.D. / Wang, Y. / Kasimova, M.A. / Carnevale, V. / Dmochowski, I.J.
History
DepositionJun 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 16, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase TEM
B: Beta-lactamase TEM
C: Beta-lactamase TEM
D: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)115,6484
Polymers115,6484
Non-polymers00
Water10,034557
1
A: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9121
Polymers28,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9121
Polymers28,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9121
Polymers28,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-lactamase TEM


Theoretical massNumber of molelcules
Total (without water)28,9121
Polymers28,9121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.500, 84.030, 94.920
Angle α, β, γ (deg.)90.00, 90.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Beta-lactamase TEM / IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 ...IRT-4 / Penicillinase / TEM-1 / TEM-16/CAZ-7 / TEM-2 / TEM-24/CAZ-6 / TEM-3 / TEM-4 / TEM-5 / TEM-6 / TEM-8/CAZ-2


Mass: 28911.904 Da / Num. of mol.: 4 / Mutation: M180T, I259L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bla, blaT-3, blaT-4, blaT-5, blaT-6 / Plasmid: pJ411 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62593, beta-lactamase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 2% (v/v) tacsimate (pH 6.0), 0.1 M BIS-TRIS (pH 6.5), 20% (w/v) PEG 3350
PH range: 6.0 - 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 1.181 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 18, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.181 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.35
ReflectionResolution: 1.82→62.92 Å / Num. obs: 82018 / % possible obs: 96.5 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.3
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.444 / % possible all: 94.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.17data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HVI
Resolution: 1.82→51.19 Å / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 36.97
RfactorNum. reflection% reflection
Rfree0.227 8375 5.18 %
Rwork0.182 --
obs0.185 81991 96.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 11.32 Å2
Refinement stepCycle: LAST / Resolution: 1.82→51.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8037 0 0 557 8594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118200
X-RAY DIFFRACTIONf_angle_d1.13511129
X-RAY DIFFRACTIONf_dihedral_angle_d13.6133053
X-RAY DIFFRACTIONf_chiral_restr0.0481292
X-RAY DIFFRACTIONf_plane_restr0.0061453
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8202-1.85160.2893840.25577501X-RAY DIFFRACTION90
1.8516-1.88530.33973930.24237522X-RAY DIFFRACTION90
1.8853-1.92150.25233440.23387674X-RAY DIFFRACTION91
1.9215-1.96080.25533930.21797533X-RAY DIFFRACTION90
1.9608-2.00340.25073360.21317655X-RAY DIFFRACTION91
2.0034-2.050.2413950.2087612X-RAY DIFFRACTION91
2.05-2.10120.24463670.20067686X-RAY DIFFRACTION91
2.1012-2.1580.24284170.19537605X-RAY DIFFRACTION90
2.158-2.22150.22414470.19127603X-RAY DIFFRACTION91
2.2215-2.29320.21564760.19437561X-RAY DIFFRACTION91
2.2932-2.37520.24743460.18247775X-RAY DIFFRACTION92
2.3752-2.47020.25824110.18917684X-RAY DIFFRACTION92
2.4702-2.58260.21154580.1797641X-RAY DIFFRACTION91
2.5826-2.71870.24413930.1887743X-RAY DIFFRACTION92
2.7187-2.8890.21964220.18277790X-RAY DIFFRACTION92
2.889-3.11190.23644030.17627744X-RAY DIFFRACTION93
3.1119-3.42480.22313690.16077840X-RAY DIFFRACTION93
3.4248-3.91980.20754170.14467764X-RAY DIFFRACTION93
3.9198-4.93620.19075020.13927811X-RAY DIFFRACTION93
4.9362-34.2310.18824570.18067801X-RAY DIFFRACTION93
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)
12.14610.1189-0.36450.86860.19540.565-0.0252-0.1298-0.09150.01630.084-0.00550.0189-0.03450.02010.03910.01840.03280.15020.05920.102922.6283-23.4251108.1826
20.7884-0.0675-0.33480.2668-0.28911.1020.0191-0.0574-0.1095-0.00330.09310.07770.0567-0.1116-0.03720.031-0.00240.00120.1288-0.00370.125713.3591-19.9061104.906
30.3325-0.08810.0120.1799-0.04320.56430.00040.06740.0629-0.00290.0083-0.0255-0.07510.0418-0.01220.0419-0.00520.04080.08640.00320.093616.5456-5.207780.44
42.5763-0.2308-0.65761.4221-0.17441.1793-0.0367-0.0502-0.1580.0159-0.08790.04510.1380.06040.06180.0445-0.00180.03680.0659-0.01170.066819.7136-10.482180.9917
51.05320.2203-0.48890.3702-0.09710.22730.0481-0.14280.04710.0477-0.0333-0.0143-0.02860.02380.0220.0173-0.0070.02050.09340.00140.08312.4679-3.564794.859
60.3683-0.4495-0.57330.66260.47151.35070.03330.02830.02420.0085-0.06720.14310.0507-0.17260.03730.0276-0.00140.01570.10880.01940.07629.4767-17.899496.7647
70.3439-0.02580.07390.06810.00080.07940.00020.0094-0.0422-0.00560.02630.0030.01580.0210.01410.01250.01070.03660.1060.01320.115819.9216-20.451492.1141
82.3320.7094-0.23651.54430.18380.6279-0.0716-0.2133-0.19360.07280.0172-0.14890.0649-0.02660.06040.04080.0380.02160.11970.01420.076128.3702-24.7196101.2181
90.6255-0.1261-0.40740.7925-0.12530.64110.00070.089-0.0205-0.035-0.0112-0.01890.02130.01760.01740.0254-0.00160.03450.1137-0.02260.09-9.3393-23.3459103.8917
100.24150.0908-0.12370.16540.060.14940.0008-0.0116-0.0333-0.00960.0443-0.0754-0.00370.07090.1620.02850.00230.03360.1261-0.00050.11080.0083-20.0755107.63
111.20490.28060.0040.33360.00561.3747-0.0045-0.06550.0840.0205-0.03960.0313-0.0823-0.0827-0.00090.0406-0.00710.03640.0544-0.00030.0908-4.1614-5.9625131.6327
121.3277-0.0448-0.44540.51010.27330.43840.01190.0720.1061-0.07920.0055-0.0287-0.06550.065-0.01570.0372-0.01770.01860.07030.01230.06970.9487-3.4857117.3182
130.7720.1044-0.01950.1950.07510.1383-0.0010.005-0.030.01650.02520.00250.0098-0.01870.02250.00710.00920.02170.08410.01390.0853-6.8497-20.8426117.7154
141.66620.6027-0.02861.135-0.22670.28790.0302-0.04050.10270.057-0.04510.0109-0.0660.0064-0.03570.05390.00070.04050.1197-0.0040.097520.7423-9.7227155.9016
150.7198-0.50050.5470.94420.16041.3786-0.06850.08140.1412-0.0590.021-0.1749-0.19120.1545-0.01330.075-0.00590.04590.09750.00480.126830.4557-12.9344152.0497
160.60030.2248-0.04580.3158-0.42030.70580.00260.0735-0.0866-0.0557-0.0184-0.0480.0957-0.008300.0383-0.00110.01320.0408-0.02120.102332.1876-25.3479128.958
172.6722-0.0830.5731.9045-0.21360.68110.00230.1308-0.17670.06130.06260.21470.1322-0.2507-0.02460.063-0.0330.03080.1356-0.01910.100918.6155-31.7167125.8014
180.48120.18250.22470.2343-0.06720.3607-0.00150.00460.0381-0.013-0.0124-0.03810.00630.0680.01950.0134-0.00390.03320.0675-0.01150.085530.3766-26.6233133.5447
191.6710.3298-0.22571.1250.08641.2528-0.0412-0.0432-0.08140.07590.06990.04230.146-0.1671-0.00170.0553-0.00170.02860.10570.00710.097228.1386-30.3632147.0156
200.97480.2571-1.01641.1163-1.54683.72360.03260.02750.066-0.0501-0.0174-0.0967-0.12490.0848-0.00570.0409-0.01230.03160.09490.00240.054833.6752-15.3571144.2362
210.70740.0593-0.36520.29940.01150.70890.0209-0.01450.04330.0104-0.00990.0178-0.0451-0.06-0.06610.0309-0.00220.03970.06430.01610.081123.4257-12.5984139.5831
220.82060.3546-0.49711.75570.27560.83010.0621-0.06550.11980.1151-0.02320.1549-0.03450.0084-0.08140.05540.02170.03750.1562-0.00050.078914.9669-8.4475148.7778
231.05670.0011-0.14591.2261-0.23871.30290.0093-0.05940.06210.0868-0.0349-0.0143-0.23270.1159-0.00250.0702-0.01250.01650.0905-0.00660.08710.485430.8924131.8002
240.5852-0.1612-0.38120.07980.08030.6274-0.04750.0541-0.0739-0.0221-0.0251-0.00140.0714-0.00310.00160.0329-0.02050.03790.0752-0.00370.082917.51916.5743106.6047
250.8043-0.1359-0.15930.3106-0.02570.5204-0.02830.007-0.0274-0.00380.00540.02270.0464-0.03390.0060.0164-0.00350.03890.0860.0070.081811.337113.6573108.2137
261.39020.8852-0.29550.7877-0.27220.09470.0297-0.1208-0.0650.0394-0.0145-0.00640.0118-0.03840.03960.0354-0.00710.0340.1201-0.0140.103113.437211.6437124.731
271.23680.6315-0.88250.7679-1.39732.81450.0817-0.14940.0531-0.0503-0.0949-0.1621-0.12670.24480.05380.0619-0.01670.03630.0945-0.0050.069619.23926.596121.9284
281.10010.067-0.64770.52170.16261.03610.0139-0.05680.10040.00790.0094-0.0205-0.0672-0.0631-0.02140.03330.00490.01650.05980.00640.076111.33131.4048111.8512
290.4697-0.1168-0.00020.36930.080.45790.0227-0.0459-0.02930.0349-00.02960.0411-0.0628-0.02790.0453-0.02440.03180.05280.020.07216.200925.4804120.5899
301.8210.312-0.21941.545-0.04331.09620.0031-0.05640.11160.06660.04360.0459-0.1702-0.0789-0.03230.061-0.00230.02370.0806-0.01190.05473.655532.0822125.2706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 26 THROUGH 50 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 51 THROUGH 68 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 69 THROUGH 118 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 119 THROUGH 131 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 132 THROUGH 179 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 180 THROUGH 195 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 196 THROUGH 271 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 272 THROUGH 290 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 26 THROUGH 50 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 51 THROUGH 68 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 69 THROUGH 131 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 132 THROUGH 179 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 180 THROUGH 290 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 26 THROUGH 50 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 51 THROUGH 68 )
16X-RAY DIFFRACTION16CHAIN 'C' AND (RESID 69 THROUGH 98 )
17X-RAY DIFFRACTION17CHAIN 'C' AND (RESID 99 THROUGH 118 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 119 THROUGH 155 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 156 THROUGH 179 )
20X-RAY DIFFRACTION20CHAIN 'C' AND (RESID 180 THROUGH 195 )
21X-RAY DIFFRACTION21CHAIN 'C' AND (RESID 196 THROUGH 271 )
22X-RAY DIFFRACTION22CHAIN 'C' AND (RESID 272 THROUGH 290 )
23X-RAY DIFFRACTION23CHAIN 'D' AND (RESID 26 THROUGH 68 )
24X-RAY DIFFRACTION24CHAIN 'D' AND (RESID 69 THROUGH 98 )
25X-RAY DIFFRACTION25CHAIN 'D' AND (RESID 99 THROUGH 155 )
26X-RAY DIFFRACTION26CHAIN 'D' AND (RESID 156 THROUGH 179 )
27X-RAY DIFFRACTION27CHAIN 'D' AND (RESID 180 THROUGH 195 )
28X-RAY DIFFRACTION28CHAIN 'D' AND (RESID 196 THROUGH 229 )
29X-RAY DIFFRACTION29CHAIN 'D' AND (RESID 230 THROUGH 251 )
30X-RAY DIFFRACTION30CHAIN 'D' AND (RESID 252 THROUGH 290 )

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