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- PDB-4cq4: C-terminal fragment of Af1503-sol: transmembrane receptor Af1503 ... -

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Basic information

Entry
Database: PDB / ID: 4cq4
TitleC-terminal fragment of Af1503-sol: transmembrane receptor Af1503 from Archaeoglobus fulgidus engineered for solubility
ComponentsENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503
KeywordsSTRUCTURAL PROTEIN / HAMP DOMAIN / TWO COMPONENT SIGNAL TRANSDUCTION / TRANSMEMBRANE SIGNALLING
Function / homology
Function and homology information


signal transduction / membrane / metal ion binding / identical protein binding
Similarity search - Function
hypothetical protein mp506/mpn330, domain 1 / hypothetical protein mp506/mpn330, domain 1 - #10 / HAMP domain / HAMP (Histidine kinases, Adenylyl cyclases, Methyl binding proteins, Phosphatases) domain / HAMP domain profile. / HAMP domain / Helix non-globular / Special
Similarity search - Domain/homology
HAMP domain-containing protein
Similarity search - Component
Biological speciesARCHAEOGLOBUS FULGIDUS (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHartmann, M.D. / Dunin-Horkawicz, S. / Hulko, M. / Martin, J. / Coles, M. / Lupas, A.N.
CitationJournal: J.Struct.Biol. / Year: 2014
Title: A Soluble Mutant of the Transmembrane Receptor Af1503 Features Strong Changes in Coiled-Coil Periodicity.
Authors: Hartmann, M.D. / Dunin-Horkawicz, S. / Hulko, M. / Martin, J. / Coles, M. / Lupas, A.N.
History
DepositionFeb 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503
B: ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503
C: ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503
D: ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503


Theoretical massNumber of molelcules
Total (without water)137,9844
Polymers137,9844
Non-polymers00
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-138.4 kcal/mol
Surface area19520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.069, 48.037, 95.187
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
ENGINEERED VERSION OF TRANSMEMBRANE RECEPTOR AF1503


Mass: 34496.090 Da / Num. of mol.: 4
Fragment: C-TERMINAL PROTEOLYTIC FRAGMENT WITH UNKNOWN CLEAVAGE SITE
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARCHAEOGLOBUS FULGIDUS (archaea) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O28769
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE STRUCTURE CONTAINS ONLY A C-TERMINAL PROTEOLYTIC FRAGMENT OF THE DEPOSITED SEQUENCE WITH ...THE STRUCTURE CONTAINS ONLY A C-TERMINAL PROTEOLYTIC FRAGMENT OF THE DEPOSITED SEQUENCE WITH UNKNOWN CLEAVAGE SITE

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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 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 25% (W/V) PEG 3350, 100 MM HEPES, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.85
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 1.7→37.7 Å / Num. obs: 43434 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.79 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 2.17 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZRX
Resolution: 1.7→37.67 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.471 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.24303 2187 5 %RANDOM
Rwork0.19286 ---
obs0.19538 41246 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.255 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å22.45 Å2
2---0.33 Å20 Å2
3----0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3060 0 0 382 3442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193098
X-RAY DIFFRACTIONr_bond_other_d0.0010.023116
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.9894206
X-RAY DIFFRACTIONr_angle_other_deg0.94737169
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.225420
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80826.26123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98315589
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3061521
X-RAY DIFFRACTIONr_chiral_restr0.110.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02581
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 165 -
Rwork0.286 2839 -
obs--94.26 %
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)
19.962-4.4618-4.43478.13293.66715.6138-0.0865-0.02570.5368-0.12360.2732-0.0982-0.5286-0.0481-0.18680.11380.0183-0.04430.04990.01060.085523.730229.808143.2424
28.0992-3.1278-10.05034.62334.325314.40220.13060.28060.1514-0.1386-0.084-0.0078-0.3402-0.1655-0.04660.038-0.0064-0.04760.06170.00880.085240.122822.078425.9714
311.3517-2.1092-10.53791.28991.401511.7637-0.1611-0.00420.01030.26670.01180.027-0.20750.02240.14930.16520.0016-0.01650.116-0.03060.099755.296115.9766.0515
48.0198-2.7927-7.26232.49424.303812.42230.1770.06190.23990.00050.0314-0.0713-0.22260.2621-0.20840.15430.00060.00070.10350.01340.142667.654112.4126-11.3617
52.73262.3266-5.86242.1934-4.459216.02870.1429-0.2386-0.00840.0791-0.0734-0.1459-0.0830.6494-0.06950.1967-0.0033-0.0160.2885-0.00710.224375.15410.0739-7.9721
64.59951.0396-6.66511.0401-0.671610.5403-0.1032-0.1577-0.2603-0.0536-0.0599-0.26960.15080.25360.16310.14390.0382-0.03640.24150.00990.161573.05633.3897-8.5345
79.09930.4742-5.42337.42041.978314.23840.08880.29210.4807-0.467-0.0359-0.0381-0.71870.1775-0.05290.1090.0152-0.06270.14580.03150.152882.98483.1063-27.3499
84.3293-3.2541-0.71392.67742.598220.7199-0.1611-0.1691-0.26780.23620.12290.15630.7337-0.14250.03810.11520.0349-0.02830.0460.02750.15127.917613.783448.2872
95.5044-0.0748-6.19061.14590.592210.8437-0.2312-0.2261-0.3290.03610.0485-0.03850.23990.53760.18270.03730.0128-0.03070.0426-0.00640.104937.62698.888427.7688
107.6989-3.1515-6.53051.82484.695413.2349-0.30740.1932-0.40790.1107-0.11540.20590.2818-0.23790.42290.13730.0012-0.04330.1061-0.02490.134952.4414.10846.5948
1110.3975-3.9551-11.10982.56015.752214.103-0.12690.1768-0.26990.1323-0.19950.16880.2545-0.29220.32640.14160.0353-0.02970.1767-0.04690.140865.5889-2.1046-9.4466
129.3007-7.8851-4.07067.66045.04826.0052-0.2450.3221-0.43120.3524-0.17570.55130.1466-0.54980.42070.18540.0092-0.05490.26980.00240.266459.5151-0.1558-16.4038
136.0827-5.1-6.79165.53795.79589.8926-0.01180.00510.04140.0944-0.01620.17650.0954-0.0670.02810.10720.0181-0.06580.146-0.00990.105263.35666.154-16.1777
1414.9309-5.2753-5.56367.52442.761511.0956-0.193-0.0697-0.45680.1481-0.0230.26520.0852-0.13920.2160.0709-0.0171-0.0630.0768-0.02020.111575.6009-4.3741-31.212
159.3545.2784-9.58275.2466-3.197812.87130.01980.58020.2898-0.6290.10950.3155-0.2324-0.923-0.12930.33910.0536-0.03760.2201-0.01090.106150.74212.4597-1.2642
165.6075-2.9473-7.72861.9523.795113.70650.2780.45760.2223-0.2345-0.113-0.1319-0.443-0.3199-0.1650.0531-0.0082-0.02550.1437-0.00030.095137.106913.896518.0144
1710.3626-0.727-12.19681.45350.990914.3731-0.13040.1321-0.0774-0.20710.032-0.08330.133-0.14650.09840.07110.0127-0.03270.0351-0.02130.072223.053718.723638.9942
1811.2675-4.3578-12.48414.49013.058714.9530.01180.3216-0.1122-0.1508-0.05770.18050.0925-0.40740.04590.0412-0.0192-0.03970.0432-0.01570.07828.817522.891254.0087
199.2909-6.1284-4.55035.55562.74463.6861-0.18380.0406-0.69040.4003-0.01840.42690.2705-0.10170.20220.1273-0.031-0.0650.0674-0.02280.19248.820115.274358.6993
2011.8525-4.687-8.41022.75472.68578.4907-0.274-0.1785-0.49760.13750.02970.19820.37040.04840.24430.0507-0.0054-0.03980.01030.00980.094713.671717.935263.2361
2114.4604-7.5521-10.66326.63597.53799.4314-0.47620.2752-1.00640.0988-0.18440.50.2413-0.47180.66060.14260.02070.02590.37950.13720.1952-1.717623.224875.9938
2210.1641-1.4343-2.99149.22491.64148.3364-0.05130.0623-0.6375-0.08880.2562-0.41550.34020.5574-0.20490.07640.0277-0.04380.2174-0.01660.111460.84735.9418.296
239.2973-3.4019-9.9181.35064.324115.2081-0.08050.02360.01890.04070.0297-0.00560.12740.27310.05080.0238-0.0046-0.04240.06350.00830.084747.760314.490125.8445
247.9325-3.3058-10.00782.60663.84112.71660.0564-0.1148-0.0143-0.0518-0.0998-0.1454-0.06420.19580.04330.03470.0274-0.0470.1069-0.0230.093533.065820.538645.9631
259.482-4.0394-11.86122.20533.438520.7631-0.0223-0.43740.04980.08350.0226-0.0866-0.07210.8699-0.00020.0929-0.0602-0.08550.15870.0440.079821.521724.268463.5256
261.34040.1575-1.39151.8572-3.07287.74470.2085-0.31540.18670.05910.0688-0.1425-0.57630.2451-0.27720.1234-0.05730.05130.0967-0.07750.144818.658132.523962.6571
275.4367-0.7981-9.28151.38461.192418.8054-0.0213-0.09560.0433-0.0380.02270.1059-0.26380.0498-0.00130.04650.0126-0.03740.0061-0.00510.056312.779130.061959.2901
289.673-0.98-11.47933.41422.310918.2550.0598-0.8820.09420.4169-0.0068-0.2594-0.35170.6393-0.0530.11310.0507-0.05420.21920.02590.10323.178431.971977.9094
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 246
2X-RAY DIFFRACTION2A247 - 266
3X-RAY DIFFRACTION3A267 - 280
4X-RAY DIFFRACTION4A281 - 297
5X-RAY DIFFRACTION5A298 - 309
6X-RAY DIFFRACTION6A310 - 326
7X-RAY DIFFRACTION7A327 - 999
8X-RAY DIFFRACTION8B1 - 246
9X-RAY DIFFRACTION9B247 - 266
10X-RAY DIFFRACTION10B267 - 280
11X-RAY DIFFRACTION11B281 - 297
12X-RAY DIFFRACTION12B298 - 309
13X-RAY DIFFRACTION13B310 - 326
14X-RAY DIFFRACTION14B327 - 999
15X-RAY DIFFRACTION15C1 - 246
16X-RAY DIFFRACTION16C247 - 266
17X-RAY DIFFRACTION17C267 - 280
18X-RAY DIFFRACTION18C281 - 297
19X-RAY DIFFRACTION19C298 - 309
20X-RAY DIFFRACTION20C310 - 326
21X-RAY DIFFRACTION21C327 - 999
22X-RAY DIFFRACTION22D1 - 246
23X-RAY DIFFRACTION23D247 - 266
24X-RAY DIFFRACTION24D267 - 280
25X-RAY DIFFRACTION25D281 - 297
26X-RAY DIFFRACTION26D298 - 309
27X-RAY DIFFRACTION27D310 - 326
28X-RAY DIFFRACTION28D327 - 999

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