[English] 日本語
Yorodumi
- PDB-1z6r: Crystal structure of Mlc from Escherichia coli -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z6r
TitleCrystal structure of Mlc from Escherichia coli
ComponentsMlc protein
KeywordsTRANSCRIPTION / transcriptional repressor / ROK family protein / DNA binding protein / helix-turn-helix / phosphotransferase system / metalloprotein
Function / homology
Function and homology information


DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / identical protein binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
ROK family / ROK family / ATPase, nucleotide binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich ...ROK family / ROK family / ATPase, nucleotide binding domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-binding transcriptional repressor Mlc
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsSchiefner, A. / Gerber, K. / Seitz, S. / Welte, W. / Diederichs, K. / Boos, W.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: The crystal structure of Mlc, a global regulator of sugar metabolism in Escherichia coli
Authors: Schiefner, A. / Gerber, K. / Seitz, S. / Welte, W. / Diederichs, K. / Boos, W.
History
DepositionMar 23, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 14, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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: Mlc protein
B: Mlc protein
C: Mlc protein
D: Mlc protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,5258
Polymers179,2634
Non-polymers2624
Water00
1
A: Mlc protein
B: Mlc protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7624
Polymers89,6322
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-20 kcal/mol
Surface area33790 Å2
MethodPISA
2
C: Mlc protein
D: Mlc protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7624
Polymers89,6322
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-18 kcal/mol
Surface area33930 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8430 Å2
ΔGint-56 kcal/mol
Surface area65360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)235.950, 74.710, 154.950
Angle α, β, γ (deg.)90.00, 129.15, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D
13A
23B
33C
43D
14A
24B
34C
44D
15A
25C
35D
45B
16A
26B
36C
46D
17A
27B
37C
47D
18A
28B
38C
48D

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNLEUAA12 - 6312 - 63
21GLNLEUBB12 - 6312 - 63
31GLNLEUCC12 - 6312 - 63
41GLNLEUDD12 - 6312 - 63
12GLYHISAA77 - 19477 - 194
22GLYHISBB77 - 19477 - 194
32GLYHISCC77 - 19477 - 194
42GLYHISDD77 - 19477 - 194
13ASPALAAA195 - 212195 - 212
23ASPALABB195 - 212195 - 212
33ASPALACC195 - 212195 - 212
43ASPALADD195 - 212195 - 212
14ARGVALAA213 - 243213 - 243
24ARGVALBB213 - 243213 - 243
34ARGVALCC213 - 243213 - 243
44ARGVALDD213 - 243213 - 243
15GLUALAAA244 - 269244 - 269
25GLUALACC244 - 269244 - 269
35GLUALADD244 - 269244 - 269
45GLUALABB244 - 269244 - 269
16SERPHEAA270 - 378270 - 378
26SERPHEBB270 - 378270 - 378
36SERPHECC270 - 378270 - 378
46SERPHEDD270 - 378270 - 378
17SERMSEAA379 - 384379 - 384
27SERMSEBB379 - 384379 - 384
37SERMSECC379 - 384379 - 384
47SERMSEDD379 - 384379 - 384
18ALAGLYAA385 - 406385 - 406
28ALAGLYBB385 - 406385 - 406
38ALAGLYCC385 - 406385 - 406
48ALAGLYDD385 - 406385 - 406

NCS ensembles :
ID
1
2
3
4
5
6
7
8

-
Components

#1: Protein
Mlc protein / Making large colonies protein


Mass: 44815.840 Da / Num. of mol.: 4 / Mutation: R52H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: mlc / Plasmid: pQE60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P50456
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 58.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M MgSO4, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97637, 0.97866
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2004
RadiationMonochromator: mirror / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.976371
20.978661
ReflectionResolution: 2.7→20 Å / Num. all: 58112 / Num. obs: 57176 / % possible obs: 98.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 66 Å2 / Rsym value: 0.105 / Net I/σ(I): 12.2
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2 / Num. unique all: 5936 / Rsym value: 0.598 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
SHELXDphasing
SHARPphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.7→19.94 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.907 / SU B: 29.571 / SU ML: 0.276 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.701 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26265 2856 5 %RANDOM
Rwork0.20266 ---
all0.20564 57155 --
obs0.20564 54299 100 %-
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 mean: 71.517 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å21.72 Å2
2--1.59 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11724 0 4 0 11728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02211912
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.9716148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.61551520
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.5824.4500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.101152108
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8541572
X-RAY DIFFRACTIONr_chiral_restr0.0940.21928
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028760
X-RAY DIFFRACTIONr_nbd_refined0.2420.26019
X-RAY DIFFRACTIONr_nbtor_refined0.3160.28152
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2455
X-RAY DIFFRACTIONr_metal_ion_refined0.0440.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.26
X-RAY DIFFRACTIONr_mcbond_it0.6641.57705
X-RAY DIFFRACTIONr_mcangle_it0.906212196
X-RAY DIFFRACTIONr_scbond_it1.47734533
X-RAY DIFFRACTIONr_scangle_it2.4074.53952
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A403medium positional0.480.5
12B403medium positional0.370.5
13C403medium positional0.380.5
14D403medium positional0.440.5
21A958medium positional0.40.5
22B958medium positional0.430.5
23C958medium positional0.560.5
24D958medium positional0.60.5
31A129medium positional0.260.5
32B129medium positional0.370.5
33C129medium positional0.280.5
34D129medium positional0.480.5
41A223medium positional0.390.5
42B223medium positional0.70.5
43C223medium positional0.310.5
44D223medium positional0.340.5
51A198medium positional0.450.5
52C198medium positional0.380.5
53D198medium positional0.660.5
54B198medium positional0.640.5
61A820medium positional0.430.5
62B820medium positional0.430.5
63C820medium positional0.420.5
64D820medium positional0.390.5
71A42medium positional0.430.5
72B42medium positional0.840.5
73C42medium positional0.560.5
74D42medium positional1.420.5
81A158medium positional0.320.5
82B158medium positional0.340.5
83C158medium positional0.320.5
84D158medium positional0.430.5
11A403medium thermal0.675
12B403medium thermal1.055
13C403medium thermal0.565
14D403medium thermal0.625
21A958medium thermal15
22B958medium thermal1.655
23C958medium thermal1.435
24D958medium thermal1.25
31A129medium thermal1.185
32B129medium thermal1.395
33C129medium thermal0.985
34D129medium thermal1.425
41A223medium thermal0.985
42B223medium thermal1.655
43C223medium thermal1.095
44D223medium thermal1.375
51A198medium thermal1.455
52C198medium thermal1.785
53D198medium thermal3.95
54B198medium thermal2.155
61A820medium thermal2.185
62B820medium thermal1.955
63C820medium thermal1.55
64D820medium thermal1.775
71A42medium thermal1.565
72B42medium thermal2.795
73C42medium thermal1.065
74D42medium thermal1.055
81A158medium thermal0.95
82B158medium thermal1.075
83C158medium thermal0.735
84D158medium thermal0.855
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 189 -
Rwork0.333 3645 -
obs--100 %
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)
17.2188-1.9190.518616.5893-0.23980.788-0.44160.91942.544-0.47810.6040.8563-1.6730.4289-0.16250.68640.04030.17990.54880.41131.291344.99977.7406-13.8049
217.3940.185-7.7814.10721.87947.3698-0.1456-0.3621-0.3742-0.3812-0.3041-0.7215-0.18490.74920.4496-0.2838-0.05640.09-0.12190.16120.104649.256218.788815.2822
311.04513.8239-1.01399.90023.34896.9668-0.35750.8868-1.542-0.12780.13631.3810.5845-1.22440.2212-0.0732-0.3338-0.06460.5715-0.0990.5189-37.0764-42.724168.6829
49.76622.2833-4.83675.0773-0.8312.4152-1.016-0.4442-0.3438-0.08550.28880.33370.8306-0.15620.72720.531-0.07660.45790.2801-0.02240.8921-30.8428-62.492357.3944
514.18231.0165-3.24945.3401-1.19778.7058-0.38230.6187-1.2981-0.19680.2642-0.09350.5611-0.26560.1181-0.31420.0280.08130.0688-0.12830.066545.9791-20.9008-6.89
65.53510.12390.93934.75190.72024.40290.0655-0.07810.3733-0.0553-0.19780.3361-0.3418-0.31480.1323-0.26510.037-0.0019-0.45710.0042-0.335720.360221.410420.0249
711.8814-0.61472.60663.94941.23949.4045-0.10480.8516-0.0136-0.06210.0786-0.0980.19890.06890.0263-0.2502-0.0196-0.0791-0.29180.0537-0.3112-12.5783-28.162775.7172
84.3344-1.3102-3.00634.8377-0.92337.4842-0.57171.4509-0.6499-1.07870.04080.9861.0385-1.52750.53090.4244-0.4209-0.12090.6774-0.360.5234-25.4505-54.846329.1501
93.83651.3313-0.23964.0157-0.32443.6512-0.10330.5402-0.2809-0.37110.0505-0.24130.3384-0.01060.0528-0.30490.0450.0096-0.284-0.0665-0.333918.583-18.03041.3447
103.32711.17010.25723.41310.51092.74390.1611-0.1441-0.00860.3943-0.246-0.04650.114-0.22090.0849-0.3332-0.0574-0.0583-0.4281-0.0111-0.291718.7888-4.550125.6745
114.96450.1313-2.69873.4774-0.29314.28490.71-0.1530.84930.10040.0290.2591-0.8839-0.2821-0.7390.0138-0.01890.15780.00010.0051-0.123-13.2357-16.684650.0584
124.89860.9149-4.44662.4629-1.12269.9359-0.03650.2957-0.08550.02760.04170.17420.3374-0.9836-0.0052-0.151-0.0288-0.1601-0.3671-0.013-0.2574-3.8659-35.965432.3682
1310.04916.0347-6.847826.4916-2.17514.8305-0.60871.28192.068-0.57241.11520.8781-0.8013-0.0183-0.5064-0.0120.16130.17160.05620.20150.302344.75-7.2083-8.5446
1416.37821.5043-8.2343.91271.31747.23890.33870.59730.1506-0.4386-0.1804-0.6246-0.83050.2257-0.1583-0.2901-0.0795-0.0062-0.30130.0025-0.20433.805918.361616.9996
1520.373711.93272.22148.19914.4648.5086-0.03390.9923-1.21760.09850.65290.7560.2034-0.7391-0.619-0.1388-0.1348-0.02550.1354-0.0946-0.0012-23.5806-35.508570.8703
167.6641-5.3761-0.07895.2841-0.97640.7044-0.79411.0083-2.00770.83390.22440.42620.7079-0.66660.56970.5805-0.23210.24290.6603-0.31540.5102-27.0889-56.263843.0193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA12 - 6312 - 63
2X-RAY DIFFRACTION2BB12 - 6312 - 63
3X-RAY DIFFRACTION3CC12 - 6312 - 63
4X-RAY DIFFRACTION4DD12 - 6312 - 63
5X-RAY DIFFRACTION5AA77 - 19477 - 194
6X-RAY DIFFRACTION6BB77 - 19477 - 194
7X-RAY DIFFRACTION7CC77 - 19477 - 194
8X-RAY DIFFRACTION8DD77 - 19477 - 194
9X-RAY DIFFRACTION9AA195 - 380195 - 380
10X-RAY DIFFRACTION10BB195 - 380195 - 380
11X-RAY DIFFRACTION11CC195 - 380195 - 380
12X-RAY DIFFRACTION12DD195 - 380195 - 380
13X-RAY DIFFRACTION13AA381 - 406381 - 406
14X-RAY DIFFRACTION14BB381 - 406381 - 406
15X-RAY DIFFRACTION15CC381 - 406381 - 406
16X-RAY DIFFRACTION16DD381 - 406381 - 406

+
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