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- PDB-7eft: Crystal structure of cell shape-determining protein MreC -

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Basic information

Entry
Database: PDB / ID: 7eft
TitleCrystal structure of cell shape-determining protein MreC
ComponentsCell shape protein MreC
KeywordsSTRUCTURAL PROTEIN / scaffold protein / dimer / filament-like structure
Function / homologyCell/Rod shape-determining protein MreC, domain 1 / Rod shape-determining protein MreC / Cell/Rod shape-determining protein MreC, domain 2 / rod shape-determining protein MreC / regulation of cell shape / membrane => GO:0016020 / Cell shape protein MreC
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsXu, Q. / Xiao, Q.J. / Sun, B.
CitationJournal: Febs Open Bio / Year: 2022
Title: The crystal structure of MreC provides insights into polymer formation.
Authors: Xu, Q. / Sun, N. / Xiao, Q. / Huang, C.Y. / Xu, M. / Zhang, W. / Li, L. / Wang, Q. / Olieric, V. / Wang, W. / He, J. / Sun, B.
History
DepositionMar 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell shape protein MreC
B: Cell shape protein MreC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2074
Polymers79,1362
Non-polymers712
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-53 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.291, 47.583, 77.332
Angle α, β, γ (deg.)90.000, 99.180, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cell shape protein MreC / Cell shape-determining protein MreC


Mass: 39568.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: mreC, A6592_13940, A9P13_02655, ACU57_14180, AM446_04030, AM464_08875, APT94_23460, AUQ13_03360, AWP75_14375, B9T59_15940, BANRA_01876, BANRA_03739, BIU72_05690, BK334_09300, BK375_18480, BMA87_ ...Gene: mreC, A6592_13940, A9P13_02655, ACU57_14180, AM446_04030, AM464_08875, APT94_23460, AUQ13_03360, AWP75_14375, B9T59_15940, BANRA_01876, BANRA_03739, BIU72_05690, BK334_09300, BK375_18480, BMA87_20860, BMT91_11345, BON83_09510, BON86_01865, BON87_17925, BUE81_20005, BvCms12BK_00952, BvCms2454_03524, BvCmsHHP001_01416, BvCmsHHP056_02431, BvCmsKKP061_00941, BvCmsKSP011_01997, BvCmsKSP024_00230, BvCmsKSP026_03280, BvCmsKSP045_01703, BvCmsKSP067_01517, BvCmsNSP047_04065, BW690_19670, BZL69_07990, C2M16_03940, C2U48_17255, C4M78_03600, C5715_13505, C5F72_02875, C5F73_03135, C5N07_22630, C6B13_17735, C7B08_03855, CA593_10025, CDL37_12575, CG692_13470, CI694_29015, CQP61_03360, CRX46_03455, CSB64_08235, CWM24_22570, D0X26_23695, D2185_00140, D3821_22845, D3822_12505, D4718_19165, D9D20_06560, D9D31_14415, D9D43_03880, D9D44_04695, D9G11_02610, D9G48_16935, D9G69_01385, D9H10_06920, D9I88_07505, D9I97_14960, D9J03_05445, D9J52_24030, DB359_11060, DBQ99_03705, DD762_12835, DJ503_15190, DL257_05935, DL326_23220, DM102_15455, DNX30_11675, DT034_24485, DTZ20_12380, DXT71_00150, DXT73_12865, E2119_16600, E2127_02840, E2128_02230, E2129_06025, E2134_15330, E2148_12755, E4K51_20900, E4K53_21150, E4K55_20750, E4K61_18265, E5S58_03200, E5S61_19155, E5S62_13475, EA214_08335, EA218_14745, EA433_04430, EAI52_13645, EC3234A_53c01270, ECONIH1_19115, ED307_14255, EEP23_08945, EI021_04350, EI028_19725, EI041_01715, EIA08_12240, EIZ93_10245, EL75_0437, EL79_0459, EL80_0450, ELV15_02095, ELV28_06610, ELX61_03590, ELX76_03650, ELY32_07020, ELY41_17630, ELY48_01450, EPT01_00130, EQ820_11810, EQ823_05315, ERS085366_00498, EST51_02480, EVY14_10875, ExPECSC038_02760, EXX71_13685, EYD11_02335, EYV18_18000, EYY27_17085, EYY34_10350, F1E19_17665, F9B07_01530, F9X20_01600, FAF34_018620, FNJ69_15130, FNW97_17800, FORC82_0511, FRV13_20275, FV293_08090, FV295_17395, FWK02_08955, FY127_07640, FZC17_06505, FZN26_16035, G5603_16305, G5608_17750, G5616_12960, G5632_04670, G5688_06165, GII66_07800, GIJ01_13225, GJ11_21070, GKF34_18720, GKF39_15510, GKF52_18305, GKF74_13415, GKF86_14680, GKF89_20670, GP689_13590, GQE22_11075, GQE33_05275, GQE34_11380, GQE42_05685, GQE64_09460, GQE68_05940, GQE87_18245, GQE88_20005, GQM17_12600, GQY14_15475, GRW05_15480, GRW42_17760, GRW57_15680, GRW80_11780, GRW81_05030, GUB08_00115, HHJ41_10835, HmCms184_00156, HmCmsJML074_01111, HV065_15440, HV109_02440, HVW04_17830, HVX17_02685, HVY77_02435, HVY93_02305, HVZ21_02645, HX136_02450, MS6198_37340, NCTC10082_02893, NCTC10090_03583, NCTC10764_03922, NCTC10963_00510, NCTC10974_00609, NCTC11022_03417, NCTC11112_00973, NCTC11126_02835, NCTC12950_00534, NCTC13216_01298, NCTC8450_05001, NCTC8500_00403, NCTC8621_00570, NCTC9007_04471, NCTC9045_00620, NCTC9050_03665, NCTC9058_01322, NCTC9062_02634, NCTC9073_00319, NCTC9117_00813, NCTC9962_00309, PGD_03866, RK56_014280, SAMEA3472044_04279, SAMEA3472080_04127, SAMEA3472110_01466, SAMEA3472112_01450, SAMEA3484427_00526, SAMEA3484429_00816, SAMEA3484434_04417, SAMEA3752372_01856, SAMEA3752559_03191, SAMEA3753097_04160, SAMEA3753300_02049, SK85_03563, WP2S18E08_04520, WP5S18E08_04820, WP7S17E04_04550, WP7S18E09_04710, WR15_24175, YDC107_1916
Production host: Escherichia coli (E. coli) / References: UniProt: A0A024L8Y8
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.53 Å3/Da / Density % sol: 19.59 %
Crystal growTemperature: 291 K / Method: evaporation
Details: 9.9% Isopropanol, 9.9% (v/v) PEG3350, 0.1M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 27893 / % possible obs: 98.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.071 / Rrim(I) all: 0.127 / Χ2: 0.431 / Net I/σ(I): 3.2 / Num. measured all: 83716
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.60.47413090.6990.3470.5910.43194
2.14-2.182.60.43513170.8050.3180.5420.4195.2
2.18-2.222.70.4214000.780.3080.5240.43396.8
2.22-2.262.60.43313520.7370.3230.5430.45598.1
2.26-2.312.70.43713600.7110.3270.5490.45298.7
2.31-2.372.90.38913840.7890.2770.480.43298.5
2.37-2.423.10.38313960.7880.2620.4660.44399.9
2.42-2.493.10.33914010.8360.230.4110.43999.9
2.49-2.563.20.32613920.8470.2190.3940.45299.6
2.56-2.653.10.28513930.8820.1920.3450.44399.9
2.65-2.743.10.25813990.9010.1750.3130.43899.6
2.74-2.8530.2214070.9150.1540.270.44199.6
2.85-2.983.20.18214050.9410.120.2190.45599.9
2.98-3.143.30.13714060.960.090.1650.456100
3.14-3.333.20.10914170.9490.0730.1310.439100
3.33-3.593.10.08614080.9850.0580.1040.45199.4
3.59-3.953.20.06714210.990.0450.0810.42699.8
3.95-4.523.30.05514090.9930.0360.0660.418100
4.52-5.6930.04814390.9950.0320.0580.35599.8
5.69-303.10.04214780.9980.0280.050.35899.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J5U

2j5u


Resolution: 2.1→29.851 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2359 2000 7.17 %
Rwork0.1865 25880 -
obs0.19 27880 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.16 Å2 / Biso mean: 38.5232 Å2 / Biso min: 15.43 Å2
Refinement stepCycle: final / Resolution: 2.1→29.851 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3285 0 2 184 3471
Biso mean--25 37.66 -
Num. residues----426
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1003-2.15280.35181310.2674170590
2.1528-2.21090.28921380.2322177496
2.2109-2.2760.28151420.2399183798
2.276-2.34940.27021400.229181098
2.3494-2.43340.27571420.21551842100
2.4334-2.53070.26191440.21871862100
2.5307-2.64580.23971430.20551855100
2.6458-2.78520.26451440.20561861100
2.7852-2.95960.2871450.20181881100
2.9596-3.18790.2271440.18951862100
3.1879-3.50820.22091450.18591872100
3.5082-4.01480.18711440.15911871100
4.0148-5.05430.20321480.14371910100
5.0543-29.8510.23531500.1769193899
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)
10.2695-0.10320.04230.07960.10960.13480.0361-0.08860.23370.03120.13230.1293-0.24110.093500.2471-0.05260.00190.24780.03920.272654.809528.838536.5104
20.1405-0.0482-0.01610.1660.01890.02570.06930.0626-0.06470.06160.21-0.07750.0974-0.2064-00.28880.01890.03850.30990.02960.253150.09113.253834.0746
30.3391-0.33940.03860.75260.2666-0.02320.00020.07370.0156-0.0044-0.02610.00280.0107-0.006-00.1340.0022-0.00820.13080.00220.137633.313515.701831.5097
40.13140.18040.08540.27110.2012-0.00040.07730.11240.0762-0.1874-0.1134-0.1259-0.04040.0621-00.20720.00770.01270.240.02860.229245.788315.987525.5311
50.42840.03610.40030.7706-0.1050.1547-0.02240.1248-0.0701-0.0253-0.07130.0282-0.1144-0.009200.1781-0.0292-0.01140.2347-0.01630.250451.176424.117934.6658
60.3309-0.0901-0.35710.4244-0.05090.5461-0.09320.0062-0.0709-0.03970.0063-0.00960.14150.0662-00.20880.0120.02920.1771-0.0030.146435.3519.591560.1056
70.06790.0592-0.23140.25380.01720.09760.07610.01670.0484-0.0634-0.0108-0.08590.0045-0.0818-00.1721-0.0053-0.0170.1702-0.00510.157623.460717.733171.6693
80.3718-0.07350.05980.67260.14960.3572-0.01580.05730.06170.049-0.04450.038-0.0409-0.003800.1444-00.00370.1398-0.00560.131424.491420.408671.4291
90.01590.02450.0074-0.00130.0198-0.0053-0.51760.0038-0.2591-0.2161-0.1853-0.16310.48530.262600.46230.10520.08690.47250.05370.368140.59458.829381.3697
100.0382-0.0117-0.02670.07560.03530.0199-0.0458-0.27440.0670.24490.312-0.2604-0.35980.3685-00.3035-0.01510.00030.3079-0.03090.31639.16223.788778.4804
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 74 through 107 )A74 - 107
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 126 )A108 - 126
3X-RAY DIFFRACTION3chain 'A' and (resid 127 through 256 )A127 - 256
4X-RAY DIFFRACTION4chain 'A' and (resid 257 through 273 )A257 - 273
5X-RAY DIFFRACTION5chain 'B' and (resid 71 through 109 )B71 - 109
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 173 )B110 - 173
7X-RAY DIFFRACTION7chain 'B' and (resid 174 through 205 )B174 - 205
8X-RAY DIFFRACTION8chain 'B' and (resid 206 through 270 )B206 - 270
9X-RAY DIFFRACTION9chain 'B' and (resid 271 through 281 )B271 - 281
10X-RAY DIFFRACTION10chain 'B' and (resid 282 through 296 )B282 - 296

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