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- PDB-9nv5: Crystal structure of phosphoglycerate mutase from Trichomonas vag... -

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Basic information

Entry
Database: PDB / ID: 9nv5
TitleCrystal structure of phosphoglycerate mutase from Trichomonas vaginalis
ComponentsPhosphoglycerate mutase
KeywordsISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / TRANSFERASE / Trichomonas vaginalis / Phosphoglycerate mutase
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / glycolytic process
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily
Similarity search - Domain/homology
Phosphoglycerate mutase
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of phosphoglycerate mutase from Trichomonas vaginalis
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionMar 20, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate mutase
B: Phosphoglycerate mutase
C: Phosphoglycerate mutase
D: Phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,74920
Polymers119,4014
Non-polymers2,34816
Water9,728540
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.780, 92.704, 94.002
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Phosphoglycerate mutase


Mass: 29850.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis G3 (eukaryote) / Gene: TVAG_165570 / Plasmid: TrvaA.01013.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A2DUN8, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)

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Non-polymers , 5 types, 556 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 540 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.69 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Index F7: 25% (w/v) PEG 3350, 0.1 M BIS-TRIS 6.5, 0.25 M ammonium sulfate. TrvaA.01013.a.B1.PW39315 at 18.8 mg/mL. plate SS Clover F4 IDX F7 BK 5 pg 18, Puck: PSL-0515, Cryo: 20% (v/v) PEG 200 + 80% crystallant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Dec 14, 2024
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.95→19.96 Å / Num. obs: 91791 / % possible obs: 99.8 % / Redundancy: 6.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.058 / Rrim(I) all: 0.15 / Χ2: 1.06 / Net I/σ(I): 11.1 / Num. measured all: 624081
Reflection shellResolution: 1.95→1.98 Å / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 1.314 / Num. measured all: 31823 / Num. unique obs: 4522 / CC1/2: 0.672 / Rpim(I) all: 0.532 / Rrim(I) all: 1.419 / Χ2: 1.02 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX(dev_5634: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→19.96 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1865 4500 4.91 %
Rwork0.1563 --
obs0.1578 91697 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7058 0 142 540 7740
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177359
X-RAY DIFFRACTIONf_angle_d1.249922
X-RAY DIFFRACTIONf_dihedral_angle_d17.6332769
X-RAY DIFFRACTIONf_chiral_restr0.0781080
X-RAY DIFFRACTIONf_plane_restr0.0111246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.970.24371710.22822895X-RAY DIFFRACTION100
1.97-20.25121640.21932868X-RAY DIFFRACTION100
2-2.020.22831560.1932870X-RAY DIFFRACTION100
2.02-2.050.22171520.19582911X-RAY DIFFRACTION100
2.05-2.070.26741510.19622897X-RAY DIFFRACTION100
2.07-2.10.22181430.19342908X-RAY DIFFRACTION100
2.1-2.130.22551370.17922869X-RAY DIFFRACTION100
2.13-2.160.23081640.17472924X-RAY DIFFRACTION100
2.16-2.20.19811460.16912885X-RAY DIFFRACTION100
2.2-2.230.19651560.16492925X-RAY DIFFRACTION100
2.23-2.270.20341460.16312880X-RAY DIFFRACTION100
2.27-2.310.18811880.1512873X-RAY DIFFRACTION100
2.31-2.360.17451610.14892873X-RAY DIFFRACTION100
2.36-2.40.21490.14162879X-RAY DIFFRACTION100
2.4-2.460.1711750.14482891X-RAY DIFFRACTION100
2.46-2.510.18851540.13922889X-RAY DIFFRACTION100
2.51-2.580.17031440.14352925X-RAY DIFFRACTION100
2.58-2.650.17611200.14022946X-RAY DIFFRACTION100
2.65-2.720.19011690.152866X-RAY DIFFRACTION100
2.72-2.810.18091460.14312938X-RAY DIFFRACTION100
2.81-2.910.18641710.14722848X-RAY DIFFRACTION100
2.91-3.030.21321260.15382956X-RAY DIFFRACTION100
3.03-3.160.20921140.15712928X-RAY DIFFRACTION100
3.16-3.330.21921310.16152940X-RAY DIFFRACTION100
3.33-3.540.18391040.16052952X-RAY DIFFRACTION99
3.54-3.810.17421650.14552889X-RAY DIFFRACTION99
3.81-4.190.15991830.13012858X-RAY DIFFRACTION99
4.19-4.790.1421640.13262916X-RAY DIFFRACTION100
4.79-60.1829960.15423009X-RAY DIFFRACTION100
6.01-19.960.1761540.18572989X-RAY DIFFRACTION100
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)
12.56640.4695-1.0613.736-0.67011.52740.0832-0.4584-0.42190.1622-0.0793-0.32860.21560.0675-0.05590.26720.002-0.0370.24390.04630.184734.6011-16.981838.5213
24.7425-1.5961-0.09813.97810.43421.1045-0.0652-0.40350.44570.16270.1516-0.4421-0.01380.2738-0.07610.1932-0.0017-0.00790.242-0.06050.199248.77128.424840.0271
32.67680.6820.66582.35190.59891.3890.1003-0.008-0.31090.13590.0094-0.17980.26640.1694-0.09250.25790.0398-0.00860.19940.00440.164644.1608-7.689833.1597
41.0179-0.2009-0.2072.84291.81052.2963-0.0009-0.09040.04740.09030.06-0.05440.02640.1363-0.1010.17850.0072-0.00680.14630.00860.130540.38372.488433.6383
51.62891.0485-2.2633.4494-2.08174.45170.554-0.4799-0.37320.46210.0798-0.62520.47510.8349-0.16530.54620.0362-0.11650.4197-0.06760.31743.985714.512257.6347
61.82970.6593-0.27593.78231.47794.1790.0895-0.02160.1997-0.0901-0.07420.0492-0.2391-0.19420.01540.25310.03180.01320.215-0.03580.250134.286217.094840.0221
72.1892.1481.69995.48022.89052.99340.1507-0.26720.11520.4583-0.1690.24570.2344-0.14070.0530.2124-0.00770.01360.1946-0.00330.182926.5780.282540.095
83.05531.1288-0.10873.83090.24142.16890.0136-0.1737-0.00530.24540.0393-0.05760.11430.0981-0.04310.20650.004-0.00960.19660.01570.163733.1064-5.183141.6084
99.54040.98970.65333.2401-0.02163.89770.1685-0.5319-0.17030.3808-0.07890.17290.10390.2031-0.10320.34540.00320.01590.2470.06880.175332.4523-13.60344.4607
102.2109-0.94111.28516.3663-0.65641.799-0.12450.18850.3329-0.02030.096-0.4334-0.41640.2409-0.02810.3179-0.02860.02660.21770.04520.195335.916315.77558.461
114.77711.31790.74723.91331.13091.3898-0.25780.3203-0.0719-0.36650.2898-0.3796-0.08190.4105-0.02490.2536-0.00370.02470.2618-0.03550.21151.1546-9.89358.7224
126.7552-4.6982-0.3253.31460.53162.73540.0032-0.08320.83270.06430.1693-0.9632-0.29970.3058-0.15320.2128-0.06530.01030.2283-0.04810.27651.696.87814.4684
131.4837-0.21880.26372.14220.16721.1911-0.04490.03090.12870.1581-0.0359-0.0171-0.1608-0.069-0.00330.2242-0.0024-0.02280.15570.0080.171837.7095.278915.1774
140.87630.0001-0.07432.03430.81971.2963-0.00670.0322-0.0499-0.02770.0788-0.04490.01930.1024-0.0450.1838-0.0069-0.00910.16430.00230.158241.7902-4.29113.9184
156.9573-1.03352.33794.9208-0.05244.39830.29780.83270.794-0.5865-0.0351-0.4174-0.41160.5906-0.28890.5208-0.05210.15640.2927-0.03930.340648.7548-16.206-9.6086
161.8236-0.6031-0.24883.89050.63913.05010.03230.0324-0.11810.0196-0.01570.12470.2367-0.1288-0.01790.2328-0.0151-0.01830.1832-0.03720.240137.2302-19.18996.9173
171.9988-2.0815-1.22214.58661.97562.07090.12280.2129-0.1502-0.3578-0.11410.28070.001-0.19060.00890.21370.0125-0.01480.20690.00630.186128.9167-2.61635.6118
181.8735-1.6367-0.02443.96440.40042.15480.03510.2283-0.0175-0.29310.03270.0135-0.0874-0.0322-0.08550.2031-0.01980.01210.18960.01980.183835.33983.13754.9646
197.5283-0.20581.08123.3646-0.41444.90020.08720.22010.0317-0.158-0.0358-0.075-0.11930.2386-0.05580.2825-0.02690.01390.20780.07120.167435.615911.52782.3196
208.35464.663-3.35015.25-2.56623.977-0.0498-0.25810.1178-0.0409-0.01520.2801-0.0478-0.3696-0.11210.2410.0582-0.02010.2949-0.08430.31831.636410.763730.9841
212.96220.5375-0.65491.9375-1.42092.5949-0.108-0.13170.10620.0784-0.02510.2295-0.2169-0.23270.10540.21620.022-0.00150.2416-0.09930.3049-0.25366.922428.1949
222.1456-0.07711.07141.6176-0.13551.0876-0.0102-0.20050.01340.1078-0.14710.26060.0761-0.23150.08550.1553-0.00290.01950.2426-0.03080.27964.39922.809330.9145
232.2521-0.8507-0.26420.60060.26352.37640.2918-1.62070.71550.4646-0.6570.5876-0.4357-0.4770.11390.71040.05640.17991.0103-0.20480.6108-2.1089.31456.1517
242.18560.3790.01232.3177-0.73443.46380.0244-0.3602-0.03880.3035-0.06480.0751-0.0086-0.07870.02320.19670.01090.02320.3066-0.02410.239612.28243.563439.4974
253.73040.4761-0.96574.0267-0.5825.08590.0271-0.0820.54710.04630.11360.2406-0.8156-0.03510.03070.38140.0356-0.01620.2382-0.08630.405211.058420.875131.4392
264.0206-4.25044.36845.5134-3.99326.02970.14810.1543-0.4783-0.0949-0.07170.61670.2466-0.3214-0.18930.2492-0.05110.03250.3201-0.06080.41234.18-14.885312.2449
275.05592.44020.26651.8768-0.59060.7526-0.33191.0020.1989-0.2194-0.09410.2462-0.1038-0.58530.37040.21440.029-0.07760.4494-0.10940.363-0.8172-4.532.3556
284.2884-3.32472.37924.795-2.48413.60430.1238-0.0822-0.98820.1081-0.04440.98270.2466-0.6105-0.03530.2228-0.05710.06160.3509-0.07110.5454-4.8337-14.244818.8226
292.1022-0.2028-0.53581.679-0.07552.37080.00360.1774-0.1102-0.0332-0.14070.27880.0109-0.13610.07190.1625-0.00380.00040.22-0.05380.29286.6368-7.725913.9007
302.3230.7808-0.9931.14460.42752.07470.87-0.4804-0.5896-0.4865-0.234-0.037-0.0912-0.4842-0.38370.8467-0.141-0.19970.929-0.16570.52222.4338-12.3643-15.2812
312.3104-0.9745-0.54541.84790.31752.87960.24130.74680.1393-0.7256-0.13880.14290.0211-0.04870.05670.41080.0938-0.10350.4972-0.00090.30498.9407-1.573-4.9179
321.6897-0.0264-0.11152.2675-0.85652.32510.02990.1689-0.0094-0.1451-0.13420.02030.0786-0.01770.090.21620.0198-0.00070.2884-0.03820.255317.4469-9.28458.4829
333.45510.72191.48114.6196-2.12557.944-0.13740.1887-0.41-0.33210.20.3130.5334-0.24610.06510.2887-0.00760.00230.2204-0.09480.404911.8555-21.92179.4867
347.1460.68651.04013.31630.0125.09630.1067-0.3866-0.6540.3654-0.18390.28590.82340.0861-0.05390.4799-0.0254-0.00440.2076-0.05780.577113.7441-27.147217.6486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 37 )
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 66 )
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 105 )
5X-RAY DIFFRACTION5chain 'A' and (resid 106 through 123 )
6X-RAY DIFFRACTION6chain 'A' and (resid 124 through 158 )
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 179 )
8X-RAY DIFFRACTION8chain 'A' and (resid 180 through 201 )
9X-RAY DIFFRACTION9chain 'A' and (resid 202 through 237 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 16 )
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 37 )
12X-RAY DIFFRACTION12chain 'B' and (resid 38 through 53 )
13X-RAY DIFFRACTION13chain 'B' and (resid 54 through 66 )
14X-RAY DIFFRACTION14chain 'B' and (resid 67 through 105 )
15X-RAY DIFFRACTION15chain 'B' and (resid 106 through 123 )
16X-RAY DIFFRACTION16chain 'B' and (resid 124 through 158 )
17X-RAY DIFFRACTION17chain 'B' and (resid 159 through 179 )
18X-RAY DIFFRACTION18chain 'B' and (resid 180 through 201 )
19X-RAY DIFFRACTION19chain 'B' and (resid 202 through 238 )
20X-RAY DIFFRACTION20chain 'C' and (resid 8 through 25 )
21X-RAY DIFFRACTION21chain 'C' and (resid 26 through 66 )
22X-RAY DIFFRACTION22chain 'C' and (resid 67 through 105 )
23X-RAY DIFFRACTION23chain 'C' and (resid 106 through 123 )
24X-RAY DIFFRACTION24chain 'C' and (resid 124 through 189 )
25X-RAY DIFFRACTION25chain 'C' and (resid 190 through 238 )
26X-RAY DIFFRACTION26chain 'D' and (resid 8 through 24 )
27X-RAY DIFFRACTION27chain 'D' and (resid 25 through 37 )
28X-RAY DIFFRACTION28chain 'D' and (resid 38 through 53 )
29X-RAY DIFFRACTION29chain 'D' and (resid 54 through 105 )
30X-RAY DIFFRACTION30chain 'D' and (resid 106 through 120 )
31X-RAY DIFFRACTION31chain 'D' and (resid 121 through 145 )
32X-RAY DIFFRACTION32chain 'D' and (resid 146 through 189 )
33X-RAY DIFFRACTION33chain 'D' and (resid 190 through 224 )
34X-RAY DIFFRACTION34chain 'D' and (resid 225 through 239 )

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