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- PDB-3ha4: Crystal structure of the type one membrane protein MIX1 from Leis... -

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Basic information

Entry
Database: PDB / ID: 3ha4
TitleCrystal structure of the type one membrane protein MIX1 from Leishmania
ComponentsMIX1
KeywordsUNKNOWN FUNCTION / TPR-like / helix-turn-helix
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #690 / Mitochondrial membrane-anchored protein / Mitochondrial membrane-anchored proteins / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / protein homodimerization activity / Mainly Alpha / CARBONATE ION / MIX domain-containing protein
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsGorman, M.A. / Walsh, P.J. / Parker, M.W.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structure of the Leishmania major MIX protein: A scaffold protein that mediates protein-protein interactions.
Authors: Gorman, M.A. / Uboldi, A.D. / Walsh, P.J. / Tan, K.S. / Hansen, G. / Huyton, T. / Ji, H. / Curtis, J. / Kedzierski, L. / Papenfuss, A.T. / Dogovski, C. / Perugini, M.A. / Simpson, R.J. / ...Authors: Gorman, M.A. / Uboldi, A.D. / Walsh, P.J. / Tan, K.S. / Hansen, G. / Huyton, T. / Ji, H. / Curtis, J. / Kedzierski, L. / Papenfuss, A.T. / Dogovski, C. / Perugini, M.A. / Simpson, R.J. / Handman, E. / Parker, M.W.
History
DepositionMay 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MIX1
B: MIX1
C: MIX1
D: MIX1
E: MIX1
F: MIX1
G: MIX1
H: MIX1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4459
Polymers141,3858
Non-polymers601
Water4,432246
1
A: MIX1
E: MIX1
hetero molecules


  • defined by author&software
  • 35.4 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)35,4063
Polymers35,3462
Non-polymers601
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-10 kcal/mol
Surface area11940 Å2
MethodPISA
2
B: MIX1
D: MIX1


Theoretical massNumber of molelcules
Total (without water)35,3462
Polymers35,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-10 kcal/mol
Surface area11420 Å2
MethodPISA
3
C: MIX1
G: MIX1


Theoretical massNumber of molelcules
Total (without water)35,3462
Polymers35,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-12 kcal/mol
Surface area10730 Å2
MethodPISA
4
F: MIX1
H: MIX1


Theoretical massNumber of molelcules
Total (without water)35,3462
Polymers35,3462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-10 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.524, 100.389, 140.651
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MIX1


Mass: 17673.150 Da / Num. of mol.: 8 / Fragment: UNP residues 46-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Strain: Friedlin / Gene: LmjF08.1200 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q4QI49
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.18M di-ammonium-hydrogen phosphate, 0.1M citric acid, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95364 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 15, 2008
RadiationMonochromator: SILICON 1 1 1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95364 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 90601 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.1827
Reflection shellResolution: 2.15→2.25 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 3.64 / Num. unique all: 8903 / % possible all: 99.3

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SHARPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→19.961 Å / SU ML: -0 / Isotropic thermal model: TLS and isotropic ADP refinement / Cross valid method: THROUGHOUT / σ(F): 1.33 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2606 2594 5.04 %RANDOM
Rwork0.2116 ---
obs0.214 51472 99.35 %-
all-0 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.02 Å2 / ksol: 0.351 e/Å3
Refinement stepCycle: LAST / Resolution: 2.4→19.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7660 0 4 246 7910
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_angle_deg1.421
X-RAY DIFFRACTIONf_bond_d0.02
X-RAY DIFFRACTIONf_dihedral_angle_d21.066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.44360.35121490.33092537X-RAY DIFFRACTION100
2.4436-2.49050.381440.32682516X-RAY DIFFRACTION100
2.4905-2.54120.33371310.26722560X-RAY DIFFRACTION100
2.5412-2.59640.31151480.25222530X-RAY DIFFRACTION100
2.5964-2.65660.30961520.24612558X-RAY DIFFRACTION100
2.6566-2.72290.32511590.24552558X-RAY DIFFRACTION100
2.7229-2.79640.28471210.252542X-RAY DIFFRACTION100
2.7964-2.87840.28461250.23652598X-RAY DIFFRACTION100
2.8784-2.9710.30321240.24782568X-RAY DIFFRACTION100
2.971-3.07680.3211330.24392554X-RAY DIFFRACTION100
3.0768-3.19960.2771230.2372598X-RAY DIFFRACTION100
3.1996-3.34450.25681530.22542554X-RAY DIFFRACTION100
3.3445-3.520.23511460.20982585X-RAY DIFFRACTION100
3.52-3.73920.26971400.19282524X-RAY DIFFRACTION98
3.7392-4.02570.19321340.172620X-RAY DIFFRACTION100
4.0257-4.42680.181300.15692606X-RAY DIFFRACTION100
4.4268-5.05820.19381090.1532654X-RAY DIFFRACTION100
5.0582-6.33880.26931440.18582653X-RAY DIFFRACTION100
6.3388-19.96150.20731290.18972563X-RAY DIFFRACTION92
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)
19.45393.23384.32553.53263.04642.7172-0.77780.57060.49650.1268-1.0901-1.0380.3120.15131.74060.31610.00670.11970.36260.14690.797474.4193-16.245317.3209
21.07730.97970.40941.4445-0.00350.0040.12890.0048-0.07280.1636-0.15690.04130.00970.07840.03190.2607-0.01880.03150.2585-0.03870.242559.0709-4.417419.3746
30.4833-0.22690.24471.57780.75920.83090.034-0.007-0.039-0.1418-0.01430.008-0.1517-0.0181-0.02730.2717-0.02390.02470.2619-0.0170.296754.3638-8.95178.871
4-3.8162-1.81851.4291-1.55470.5512-0.9580.10580.2572-0.19030.10970.11030.9778-0.0084-0.0105-0.08910.5632-0.0862-0.03670.72710.05721.05258.3897-19.807821.7633
50.13810.21790.12660.44711.26871.56470.0975-0.0155-0.1858-0.3084-0.13480.03980.2722-0.19770.210.3029-0.0405-0.01570.20390.0110.436547.4241-18.41248.3249
6-0.81614.3395-2.56775.5337-8.58394.0885-1.1051-0.1896-0.4977-0.2545-0.4036-1.03090.5165-0.41751.49311.12950.0992-0.15330.9503-0.37430.886289.079425.741842.8689
70.31990.4336-1.48251.81690.33240.7972-0.03750.1549-0.1143-0.0321-0.0361-0.15780.2562-0.15360.01130.3329-0.0287-0.0610.38410.04350.329686.813739.640553.0322
8-0.3530.9599-0.43111.34330.21311.4778-0.09160.0805-0.0103-0.01440.12330.13930.1674-0.2164-0.00360.2614-0.0454-0.06070.28890.01490.32883.431934.550557.5552
9-0.83763.1598-8.3707-1.1232-0.30061.1051.22021.10811.0450.16470.14231.3078-0.172-1.2747-1.36690.38760.13-0.17480.75240.17860.746870.567338.539861.6472
10-0.23210.30810.06042.1043-1.08430.61820.12710.0194-0.294-0.0584-0.01760.0630.11040.0082-0.09340.2781-0.0245-0.01620.24590.02370.335887.520528.527966.7559
11-0.0158-0.78540.06941.4207-0.38380.78510.17830.1084-0.0584-0.1965-0.07190.35220.1178-0.0823-0.09390.33710.0287-0.04130.25220.04740.273945.751332.63624.8416
123.2893-7.4795-3.44656.0932-2.65997.3019-1.7225-0.4899-1.6015-0.7173-0.02511.2487-0.0615-0.36061.70230.379-0.0136-0.08370.30510.03480.835236.040627.0204-2.1998
130.36480.42190.22311.23930.10360.13340.01530.01480.1244-0.1311-0.0486-0.0307-0.18580.0410.03360.38580.0305-0.0040.31480.02460.328746.386823.95733.3968
140.9650.04770.12190.0935-1.0602-2.78210.8109-0.2692-0.037-0.3464-0.94220.0988-0.24870.09440.07570.785-00.00060.4419-0.03960.326243.445218.3669-9.9355
151.1021-0.20220.05681.6333-1.3437-0.508-0.12140.0285-0.1861-0.1461-0.0628-0.08840.09670.08860.17380.31970.0509-0.03060.27530.0330.268647.055315.232910.0079
161.0602-0.08240.02271.64931.1135-0.7836-0.110.00050.0821-0.69780.05090.0908-0.0980.18380.07820.44970.0445-0.03070.31720.00340.26746.51135.748767.8555
17-2.31960.91060.92934.6104-0.1673.4597-0.12720.05670.12140.0279-0.29460.5191-0.08990.33920.48981.0529-0.0709-0.08030.6147-0.13540.666639.7316-3.972965.1651
18-0.1212-0.7684-0.04841.6920.63910.91850.06110.02750.0287-0.1872-0.04370.0505-0.1299-0.257-0.01930.21020.00750.02490.1880.00760.181949.93180.381274.1664
190.3192-0.2695-0.04831.62521.31161.8010.03120.068-0.18940.04270.1312-0.47120.17410.0982-0.13370.1773-0.0022-0.0360.17230.03230.257854.065-4.374878.413
200.2376-1.7211.48381.0773-0.84020.71590.0153-0.0813-0.023-0.01650.0857-0.17750.1607-0.0259-0.13110.2808-0.02570.00840.2963-0.00010.245452.01173.527684.6162
210.2474-1.053-1.5667-0.7891-0.6882-0.45580.1594-0.5247-0.6049-0.1446-0.0016-0.15570.15750.2383-0.14810.43580.21560.02550.67360.0020.624755.120129.87251.447
222.30220.37462.00887.9208-4.19423.32750.48421.30040.18030.8032-0.4345-0.7735-0.38010.2756-0.10650.53290.09080.03920.6982-0.0560.490660.354741.774353.4313
230.8011-0.5199-1.55432.9166-0.410.54150.22610.3105-0.0176-0.2182-0.2362-0.52380.08320.1865-0.01560.24890.04560.08770.49380.00170.330154.500439.026640.9521
241.3653-3.47871.82781.25550.26151.59530.75251.8597-1.3417-0.07350.03140.7649-0.1028-0.4594-0.76450.42160.1149-0.13890.6823-0.22110.510943.395426.418441.4884
250.0007-1.03540.33041.14120.9430.77340.07311.0831-0.0196-0.1556-0.10390.1919-0.2205-0.28260.05430.32170.03020.01280.54370.07920.275641.649342.756939.3384
263.27454.14740.91993.02194.4363.7158-0.6136-0.09090.0009-1.0883-0.63470.4362-0.50890.51051.32811.05180.2017-0.53561.0414-0.15051.00951.852224.901428.4176
270.5752-0.4941.11530.6399-0.75331.5495-0.0345-0.1681-0.02890.07580.0144-0.0694-0.2362-0.16280.0150.2909-0.0166-0.02930.2523-0.02670.261563.32696.566526.5644
280.7261-0.0772-0.1640.45380.27930.21760.0747-0.01570.1576-0.27650.1529-0.1752-0.24470.071-0.19190.3818-0.05250.05720.2754-0.06040.329773.192914.973327.4381
292.15636.06254.26985.68023.34847.83191.51160.5577-0.3671-0.3003-0.9233-0.8882-0.5853-0.4347-0.63390.53980.0360.01180.6464-0.11920.655759.266113.459936.3287
302.14771.49291.94923.3849-2.1211-3.90080.2899-0.5568-0.26050.5898-0.2057-0.2828-0.49320.1445-0.03390.2656-0.08520.01390.2962-0.1380.246576.570318.648538.8754
312.72141.473-5.70984.15484.96242.77730.0741-0.45120.1295-0.69060.4665-0.1281-0.55170.6389-0.50440.67430.17820.15310.5864-0.03410.536768.4303-35.669246.323
320.12471.0118-1.46811.9786-0.20732.1303-0.1693-0.2715-0.1122-0.17740.1546-0.297-0.06450.23670.00040.3074-0.05970.08920.345-0.04560.291364.6981-27.591256.0329
330.7336-0.1021-1.11491.94260.01980.38470.3007-0.03250.0055-0.31430.1696-0.2671-0.13780.1796-0.53930.4873-0.15930.01630.4362-0.03510.430566.1706-16.618658.3155
343.6143-3.6471-3.05294.14062.2542-2.60750.48951.45040.1318-0.8113-0.3819-0.2238-0.2857-0.5267-0.06430.81080.1621-0.06560.50860.03330.330749.7673-20.545349.2258
355.10771.90842.5113-3.05340.06395.69710.7156-0.02230.64570.0271-0.07030.0217-0.7120.0431-0.5930.6638-0.14750.04580.3007-0.07920.483958.2435-11.226859.6096
364.1025-0.1108-0.44264.6322-5.5832-2.91390.17270.11840.43011.026-0.61630.2248-0.69-0.02540.41560.599-0.1759-0.20010.4702-0.0140.537177.07889.924750.6048
37-0.17831.4213-0.46281.69250.37090.2916-0.1768-0.338-0.3018-0.31651.0556-0.2312-0.01090.0152-0.82970.4922-0.0818-0.20420.6171-0.00010.77285.10344.241342.6643
380.52170.2113-0.26681.5452-0.2811-1.3155-0.03970.0609-0.05440.2129-0.106-0.1650.10910.04270.18430.3969-0.0686-0.11250.35010.08220.311875.57170.335646.8178
39-1.9928-0.1854-0.62530.41420.0240.3262-0.28720.1869-0.4942-0.00750.0335-0.51140.040.56480.25750.58280.0901-0.12920.88820.09011.002486.0433-9.404342.563
400.25080.8731-0.56190.773-0.9835-0.58830.13-0.20060.0708-0.0038-0.03310.14450.1445-0.0204-0.10080.4274-0.0199-0.02310.37750.0220.338965.7865-2.884443.6241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 59:64)
2X-RAY DIFFRACTION2chain A and resid 65:89)
3X-RAY DIFFRACTION3chain A and resid 90:155)
4X-RAY DIFFRACTION4chain A and resid 156:161)
5X-RAY DIFFRACTION5chain A and resid 162:184)
6X-RAY DIFFRACTION6chain B and resid 65:71)
7X-RAY DIFFRACTION7chain B and resid 72:87)
8X-RAY DIFFRACTION8chain B and resid 88:122)
9X-RAY DIFFRACTION9chain B and resid 123:133)
10X-RAY DIFFRACTION10chain B and resid 134:184)
11X-RAY DIFFRACTION11chain C and resid 69:84)
12X-RAY DIFFRACTION12chain C and resid 85:89)
13X-RAY DIFFRACTION13chain C and resid 90:122)
14X-RAY DIFFRACTION14chain C and resid 123:133)
15X-RAY DIFFRACTION15chain C and resid 134:183)
16X-RAY DIFFRACTION16chain D and resid 71:88)
17X-RAY DIFFRACTION17chain D and resid 89:94)
18X-RAY DIFFRACTION18chain D and resid 95:126)
19X-RAY DIFFRACTION19chain D and resid 127:155)
20X-RAY DIFFRACTION20chain D and resid 156:184)
21X-RAY DIFFRACTION21chain E and resid 70:84)
22X-RAY DIFFRACTION22chain E and resid 85:94)
23X-RAY DIFFRACTION23chain E and resid 95:153)
24X-RAY DIFFRACTION24chain E and resid 154:162)
25X-RAY DIFFRACTION25chain E and resid 163:180)
26X-RAY DIFFRACTION26chain F and resid 55:61)
27X-RAY DIFFRACTION27chain F and resid 62:89)
28X-RAY DIFFRACTION28chain F and resid 90:154)
29X-RAY DIFFRACTION29chain F and resid 155:161)
30X-RAY DIFFRACTION30chain F and resid 162:183)
31X-RAY DIFFRACTION31chain G and resid 69:73)
32X-RAY DIFFRACTION32chain G and resid 74:116)
33X-RAY DIFFRACTION33chain G and resid 117:155)
34X-RAY DIFFRACTION34chain G and resid 156:166)
35X-RAY DIFFRACTION35chain G and resid 167:182)
36X-RAY DIFFRACTION36chain H and resid 72:79)
37X-RAY DIFFRACTION37chain H and resid 80:95)
38X-RAY DIFFRACTION38chain H and resid 96:122)
39X-RAY DIFFRACTION39chain H and resid 123:137)
40X-RAY DIFFRACTION40chain H and resid 138:180)

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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

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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

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