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- PDB-9zax: Crystal structure of Phosphoglycerate mutase from Trichomonas vag... -

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Basic information

Entry
Database: PDB / ID: 9zax
TitleCrystal structure of Phosphoglycerate mutase from Trichomonas vaginalis in complex with 3-phosphoglyceric acid
ComponentsPhosphoglycerate mutase
KeywordsISOMERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / TRANSFERASE / Phosphoglycerate mutase
Function / homology
Function and homology information


phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / phosphoglycerate mutase activity / canonical glycolysis / cytosol
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
3-PHOSPHOGLYCERIC ACID / Phosphoglycerate mutase
Similarity search - Component
Biological speciesTrichomonas vaginalis G3 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 in complex with 3-phosphoglyceric acid
Authors: Seibold, S. / Lovell, S. / Battaile, K.P.
History
DepositionNov 19, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 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)122,73323
Polymers119,7174
Non-polymers3,01619
Water8,197455
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)74.639, 93.061, 95.485
Angle α, β, γ (deg.)90.00, 92.86, 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: 29929.199 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)
References: UniProt: A2DUN8, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent)

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Non-polymers , 5 types, 474 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID


Mass: 186.057 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7O7P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 455 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Index F7 : 250 mM AMSO4, 0.1M Bis-Tris pH 6.5, 25% PEG 3350. TrvaA.01013.a.B1.PW39315 at 18.8 mg/mL. plate SS Clover F4 IDX F7 BK 5 pg 18, overnight soak in 2mM 3PG in crystallant. Puck: PSL- ...Details: Index F7 : 250 mM AMSO4, 0.1M Bis-Tris pH 6.5, 25% PEG 3350. TrvaA.01013.a.B1.PW39315 at 18.8 mg/mL. plate SS Clover F4 IDX F7 BK 5 pg 18, overnight soak in 2mM 3PG in crystallant. Puck: PSL-1001, 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: Jun 7, 2025
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: 2.1→48.83 Å / Num. obs: 76013 / % possible obs: 99.8 % / Redundancy: 4.3 % / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.077 / Rrim(I) all: 0.16 / Χ2: 1.02 / Net I/σ(I): 8.3 / Num. measured all: 327122
Reflection shellResolution: 2.1→2.14 Å / % possible obs: 99.9 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.95 / Num. measured all: 19062 / Num. unique obs: 4503 / CC1/2: 0.51 / Rpim(I) all: 0.523 / Rrim(I) all: 1.089 / Χ2: 1.06 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5882: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.83 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2126 3501 4.61 %
Rwork0.1779 --
obs0.1796 75976 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7180 0 139 455 7774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047479
X-RAY DIFFRACTIONf_angle_d0.71610105
X-RAY DIFFRACTIONf_dihedral_angle_d18.0952777
X-RAY DIFFRACTIONf_chiral_restr0.0451104
X-RAY DIFFRACTIONf_plane_restr0.0061272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.29131280.25522910X-RAY DIFFRACTION100
2.13-2.160.29451260.24512903X-RAY DIFFRACTION100
2.16-2.190.27951310.2392906X-RAY DIFFRACTION100
2.19-2.230.28221420.2292876X-RAY DIFFRACTION100
2.23-2.260.25771550.22342899X-RAY DIFFRACTION100
2.26-2.30.25011150.20422860X-RAY DIFFRACTION100
2.3-2.340.28041180.2012948X-RAY DIFFRACTION100
2.34-2.390.28491130.19732942X-RAY DIFFRACTION100
2.39-2.440.22491200.18392848X-RAY DIFFRACTION100
2.44-2.490.24221490.18292899X-RAY DIFFRACTION100
2.49-2.550.19181570.17942870X-RAY DIFFRACTION100
2.55-2.610.24081460.18532859X-RAY DIFFRACTION100
2.61-2.680.21431310.18252923X-RAY DIFFRACTION100
2.68-2.760.22491660.17922878X-RAY DIFFRACTION100
2.76-2.850.21091820.18642839X-RAY DIFFRACTION100
2.85-2.950.23171360.18412918X-RAY DIFFRACTION100
2.95-3.070.22181100.17862912X-RAY DIFFRACTION100
3.07-3.210.21191480.18392886X-RAY DIFFRACTION100
3.21-3.380.22441510.18932889X-RAY DIFFRACTION100
3.38-3.590.21341470.17552910X-RAY DIFFRACTION100
3.59-3.870.1811560.15392876X-RAY DIFFRACTION99
3.87-4.260.14821250.13722903X-RAY DIFFRACTION99
4.26-4.870.16381390.13382920X-RAY DIFFRACTION100
4.87-6.140.19321290.16552954X-RAY DIFFRACTION100
6.14-48.830.21661810.18822947X-RAY DIFFRACTION99
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)
10.36521.08270.20054.3421-0.11431.66580.0604-0.1959-0.1467-0.0595-0.1-0.27870.04010.01520.01890.2576-0.0111-0.00760.23320.04220.2497-3.3484-17.381538.6864
23.6027-1.1532-0.75283.50771.70191.3414-0.1428-0.25160.09970.34960.2555-0.28670.03280.4165-0.10860.25540.012-0.01280.2357-0.04030.230212.47849.270340.0772
32.4214-0.12010.0122.69830.46011.88170.0602-0.0109-0.12890.11170.0001-0.18920.21590.2014-0.06880.21040.0133-0.02940.162-0.00870.15537.7444-6.828533.5464
40.8571-0.0945-0.33151.77910.81361.39920.0193-0.03740.04170.0070.0403-0.1382-0.02130.0613-0.050.18290.0133-0.01040.14340.00130.17584.00323.368933.9937
52.80010.40490.55262.39071.30682.90990.1655-0.2964-0.09740.40690.0665-0.33130.38070.1236-0.21290.4120.0271-0.04930.2613-0.06940.26495.494916.961153.6988
62.13740.6237-0.4972.0411-0.08613.8852-0.00330.3470.0847-0.3116-0.08860.0479-0.0205-0.27720.06590.290.04250.00680.2215-0.02370.2663-4.131317.229535.3728
72.40342.38591.70986.41282.84132.41880.1549-0.19340.20030.4045-0.25250.46090.0941-0.36020.09980.2198-0.01430.01440.2258-0.00720.2013-9.61681.305540.7926
82.39881.0936-0.94723.12620.50912.42090.022-0.20660.04330.2271-0.02230.00910.10650.1546-0.01510.1880.0245-0.03890.15850.00890.1477-3.1063-4.193242.2436
96.35310.81570.33782.1892-0.29353.51550.1544-0.70340.25480.3822-0.1894-0.00490.0490.10680.02810.3429-0.0164-0.01360.24370.0420.1993-3.0227-11.377946.692
100.7795-1.4044-0.34344.7907-0.89071.6972-0.16830.30460.18770.46780.0113-0.3102-0.34670.14180.13910.3180.016-0.04460.20310.03730.241-2.03817.35149.0101
112.0802-0.5577-0.07832.97431.07860.97940.02670.05130.006-0.13550.1141-0.3541-0.12410.206-0.14590.1999-0.01850.02670.1929-0.0060.180411.0458-0.104612.3841
120.65070.39590.01181.88471.01731.45170.00680.0842-0.0096-0.0390.0911-0.1746-0.0230.1883-0.08080.19950.0016-0.00580.1736-0.00010.16535.0374-3.631414.1467
136.0451-1.65671.50166.1045-0.31614.83150.18450.68540.4602-0.19890.0369-0.4376-0.33440.3795-0.2520.4222-0.06440.12460.2988-0.05160.344511.9118-16.0186-8.9495
140.9221-0.9647-0.13843.2740.14830.81750.04270.0715-0.0869-0.10330.01980.054-0.0003-0.0547-0.06840.1575-0.0083-0.01830.1755-0.00270.1469-2.6539-7.38376.3785
154.29710.03370.93181.9327-0.08053.9160.2090.4117-0.0891-0.3394-0.0411-0.0352-0.0150.1376-0.17830.3520.01180.02310.25230.08310.2158-1.204511.12731.2426
166.87766.9575-5.70887.4064-5.00876.37290.5301-0.13640.80790.424-0.23780.6552-0.6099-0.1829-0.35890.28920.0729-0.01650.3354-0.03280.4357-33.626512.957830.9871
174.1948-1.0870.21451.3391-1.09891.0395-0.1217-1.00410.03080.28860.10950.4933-0.4237-0.7150.05920.29870.01050.06910.5385-0.07810.3722-40.06472.343140.878
185.34262.6448-2.46826.0154-3.13016.17170.26140.60230.57350.03880.16220.7928-0.4215-0.8398-0.32530.25090.099-0.01310.3578-0.01610.4673-42.14911.210123.6793
192.01880.1802-0.19021.68860.53972.04480.0743-0.0268-0.0098-0.2359-0.25570.0508-0.057-0.11810.14290.19920.0367-0.02210.2836-0.01040.3003-31.83996.766624.9761
201.82820.31130.16321.6905-0.71091.39490.1854-0.28160.21260.1509-0.12570.2435-0.1634-0.501-0.13930.1849-0.00290.00880.3006-0.03490.2545-30.09563.966634.9593
214.02021.06260.03720.75370.73191.10280.679-1.04721.06660.2605-0.79910.50230.0927-0.11150.00430.80660.05590.11591.0536-0.25660.7109-38.083510.960757.0667
224.16071.3690.06944.56540.15873.91890.2377-0.9749-0.08830.8385-0.35190.50590.419-0.3530.1160.4232-0.08440.10910.6226-0.01060.3004-31.26651.727452.8845
232.11870.59530.08242.278-0.52463.10140.0305-0.25560.17240.0974-0.05410.0372-0.1547-0.02480.04130.2180.02390.00020.2757-0.03450.2769-22.86167.88337.2291
243.7586-0.00480.7332.28811.22344.05080.1365-0.2470.72040.0206-0.08970.1634-0.76230.005-0.02130.5320.04720.01780.2533-0.0450.5938-26.107923.549330.2633
252.2369-0.4204-0.04611.8555-0.52872.33470.00440.269-0.2652-0.1183-0.11970.16150.2122-0.37590.07190.1834-0.0069-0.00720.3022-0.06060.2757-34.8435-11.009814.4242
261.89670.1066-0.1981.2067-0.1650.04010.09520.3676-0.0688-0.089-0.13430.2106-0.0602-0.25370.01790.16380.0413-0.01270.3199-0.01610.2404-30.9049-5.368912.8878
272.9897-0.96880.14910.36980.04190.345-0.13270.9539-0.5774-0.2347-0.07770.2396-0.3039-0.14430.32440.7538-0.0161-0.07940.8612-0.12050.5455-34.5728-12.6796-12.5599
284.367-1.79440.7353.9331-1.35224.55820.26371.07390.0778-0.6045-0.36780.1458-0.0288-0.54070.06260.41190.04640.01290.74310.07480.2872-28.3274-3.7211-8.0056
291.6915-0.0745-0.52342.0043-0.40592.16890.05710.2503-0.0742-0.1429-0.10650.0623-0.0055-0.15610.03740.1910.0277-0.00830.3105-0.03310.2403-21.1937-8.64468.3757
306.9248-0.4746-0.25693.52561.01344.2665-0.1216-0.0465-0.8644-0.1288-0.02510.3030.5194-0.40380.11570.3698-0.0472-0.0190.2521-0.07490.5285-25.1727-24.690416.2563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 15 )
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 138 )
6X-RAY DIFFRACTION6chain 'A' and (resid 139 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 238 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 15 )
11X-RAY DIFFRACTION11chain 'B' and (resid 17 through 66 )
12X-RAY DIFFRACTION12chain 'B' and (resid 67 through 105 )
13X-RAY DIFFRACTION13chain 'B' and (resid 106 through 123 )
14X-RAY DIFFRACTION14chain 'B' and (resid 124 through 201 )
15X-RAY DIFFRACTION15chain 'B' and (resid 202 through 237 )
16X-RAY DIFFRACTION16chain 'C' and (resid 7 through 24 )
17X-RAY DIFFRACTION17chain 'C' and (resid 25 through 37 )
18X-RAY DIFFRACTION18chain 'C' and (resid 38 through 53 )
19X-RAY DIFFRACTION19chain 'C' and (resid 54 through 79 )
20X-RAY DIFFRACTION20chain 'C' and (resid 80 through 105 )
21X-RAY DIFFRACTION21chain 'C' and (resid 106 through 123 )
22X-RAY DIFFRACTION22chain 'C' and (resid 124 through 138 )
23X-RAY DIFFRACTION23chain 'C' and (resid 139 through 201 )
24X-RAY DIFFRACTION24chain 'C' and (resid 202 through 237 )
25X-RAY DIFFRACTION25chain 'D' and (resid 7 through 66 )
26X-RAY DIFFRACTION26chain 'D' and (resid 67 through 105 )
27X-RAY DIFFRACTION27chain 'D' and (resid 106 through 123 )
28X-RAY DIFFRACTION28chain 'D' and (resid 124 through 138 )
29X-RAY DIFFRACTION29chain 'D' and (resid 139 through 200 )
30X-RAY DIFFRACTION30chain 'D' and (resid 201 through 238 )

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