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- PDB-9mmh: HFP (histidine family phosphatase) that catalyzes essential depho... -

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Basic information

Entry
Database: PDB / ID: 9mmh
TitleHFP (histidine family phosphatase) that catalyzes essential dephosphorylation for riboflavin biosynthesis
ComponentsPhosphoglycerate mutase
KeywordsHYDROLASE / riboflavin / phosphatase
Function / homology: / Phosphoglycerate mutase family / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / phosphatase activity / membrane / cytoplasm / Phosphoglycerate mutase
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsHoffpauir, Z.A. / Meneely, K.M. / Lamb, A.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2204080 United States
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Identification of the phosphatase essential for riboflavin biosynthesis in Aquifex aeolicus.
Authors: Hoffpauir, Z.A. / Lamb, A.L.
History
DepositionDec 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)95,95915
Polymers94,9024
Non-polymers1,05711
Water7,026390
1
A: Phosphoglycerate mutase
B: Phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9317
Polymers47,4512
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-70 kcal/mol
Surface area17450 Å2
MethodPISA
2
C: Phosphoglycerate mutase
hetero molecules

D: Phosphoglycerate mutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0288
Polymers47,4512
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_444x-y-1,-y-1,-z-1/31
Buried area2890 Å2
ΔGint-90 kcal/mol
Surface area17420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.015, 110.015, 256.654
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein
Phosphoglycerate mutase


Mass: 23725.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: gpmA, aq_1744 / Production host: Escherichia coli (E. coli) / References: UniProt: O67630
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Tris-HCl pH 8.5, 2 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.04→39.02 Å / Num. obs: 115401 / % possible obs: 99.9 % / Redundancy: 20 % / Biso Wilson estimate: 32.51 Å2 / Rpim(I) all: 0.034 / Net I/σ(I): 17.2
Reflection shellResolution: 2.04→2.07 Å / Num. unique obs: 5580 / Rpim(I) all: 0.637

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Processing

Software
NameVersionClassification
AutoSol1.20.1_4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: SAD / Resolution: 2.04→39.02 Å / SU ML: 0.232 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.4714
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2252 2006 1.74 %
Rwork0.19 113246 -
obs0.1906 115252 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.02 Å2
Refinement stepCycle: LAST / Resolution: 2.04→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6668 0 55 390 7113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01316858
X-RAY DIFFRACTIONf_angle_d1.28079231
X-RAY DIFFRACTIONf_chiral_restr0.06661013
X-RAY DIFFRACTIONf_plane_restr0.01311155
X-RAY DIFFRACTIONf_dihedral_angle_d15.22462617
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.04-2.090.31481400.28287877X-RAY DIFFRACTION98.72
2.09-2.150.26361430.23157995X-RAY DIFFRACTION100
2.15-2.210.28661400.22528030X-RAY DIFFRACTION100
2.21-2.280.27621400.21817976X-RAY DIFFRACTION99.93
2.28-2.360.23721420.21648019X-RAY DIFFRACTION99.99
2.36-2.460.241430.20098036X-RAY DIFFRACTION99.95
2.46-2.570.24631400.20358051X-RAY DIFFRACTION99.95
2.57-2.70.22751420.19748052X-RAY DIFFRACTION99.96
2.7-2.870.22571470.21148067X-RAY DIFFRACTION99.99
2.87-3.090.26531430.19638098X-RAY DIFFRACTION99.99
3.09-3.410.21391430.19818154X-RAY DIFFRACTION100
3.41-3.90.20021420.16518134X-RAY DIFFRACTION99.81
3.9-4.910.1691460.14748225X-RAY DIFFRACTION99.93
4.91-39.020.24441550.19558532X-RAY DIFFRACTION99.86

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