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- PDB-9qcj: Crystal structure of PhoC wild type acid phosphatase -

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Basic information

Entry
Database: PDB / ID: 9qcj
TitleCrystal structure of PhoC wild type acid phosphatase
ComponentsMajor phosphate-irrepressible acid phosphatase
KeywordsBIOSYNTHETIC PROTEIN / Acid phosphatase
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space
Similarity search - Function
: / Acid phosphatase, class A, bacterial, conserved site / Class A bacterial acid phosphatases signature. / Acid phosphatase, class A, bacterial / Acid phosphatase homologues / Phosphatidic acid phosphatase type 2/haloperoxidase / PAP2 superfamily / Phosphatidic acid phosphatase type 2/haloperoxidase superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Major phosphate-irrepressible acid phosphatase
Similarity search - Component
Biological speciesMorganella morganii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsLevy, C.W. / Ortmayer, M.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MR/T041722/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/W029324/1 United Kingdom
Citation
Journal: Nat Commun / Year: 2025
Title: Enzymatic synthesis of key RNA therapeutic building blocks using simple phosphate donors.
Authors: Meng, Q. / Benckendorff, C. / Morrill, C. / Zhuo, Y. / Egerstrom, A. / Ni Cheallaigh, A. / Derrington, S.R. / Obexer, R. / Ortmayer, M. / Levy, C.W. / Finnigan, J.D. / Charnock, S.J. / ...Authors: Meng, Q. / Benckendorff, C. / Morrill, C. / Zhuo, Y. / Egerstrom, A. / Ni Cheallaigh, A. / Derrington, S.R. / Obexer, R. / Ortmayer, M. / Levy, C.W. / Finnigan, J.D. / Charnock, S.J. / Turner, N.J. / Miller, G.J. / Lovelock, S.L.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMar 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major phosphate-irrepressible acid phosphatase
B: Major phosphate-irrepressible acid phosphatase
C: Major phosphate-irrepressible acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6147
Polymers81,2233
Non-polymers3914
Water1,40578
1
A: Major phosphate-irrepressible acid phosphatase
B: Major phosphate-irrepressible acid phosphatase
C: Major phosphate-irrepressible acid phosphatase
hetero molecules

A: Major phosphate-irrepressible acid phosphatase
B: Major phosphate-irrepressible acid phosphatase
C: Major phosphate-irrepressible acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,22914
Polymers162,4476
Non-polymers7828
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Unit cell
Length a, b, c (Å)116.380, 116.380, 94.540
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 21 through 82 or resid 84 through 151 or resid 159 through 246))
d_2ens_1(chain "B" and (resid 21 through 82 or resid 84...
d_3ens_1(chain "C" and (resid 21 through 82 or resid 84...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ALAALAALAALAAA21 - 8221 - 82
d_12ALAALAASNASNAA84 - 15184 - 151
d_13SERSERLYSLYSAA159 - 246159 - 246
d_21ALAALAALAALABB21 - 8221 - 82
d_22ALAALAASNASNBB84 - 15184 - 151
d_23SERSERLYSLYSBB159 - 246159 - 246
d_31ALAALAALAALACC21 - 8221 - 82
d_32ALAALAASNASNCC84 - 15184 - 151
d_33SERSERLYSLYSCC159 - 246159 - 246

NCS oper:
IDCodeMatrixVector
1given(-0.0890358203165, 0.276759853551, -0.956805417085), (-0.206195982967, 0.934689176665, 0.289550271342), (0.974451558216, 0.223069779415, -0.0261540475367)-40.4617161676, 9.49079012535, -8.59298476735
2given(0.290746055717, 0.0657621502484, 0.954537621406), (0.917118262835, 0.265175350735, -0.297617414371), (-0.272691809667, 0.961954974496, 0.0167870183035)-40.6436483647, 9.73648018652, -9.14298261739

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Components

#1: Protein Major phosphate-irrepressible acid phosphatase / HPAP


Mass: 27074.486 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Morganella morganii (bacteria) / Gene: phoC / Production host: Escherichia coli (E. coli) / References: UniProt: P28581, acid phosphatase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M Phosphate citrate pH 5.5 30% v/v Peg smear low
Temp details: Chilled imaging hotel

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.24→50.39 Å / Num. obs: 49424 / % possible obs: 99.98 % / Redundancy: 19.6 % / Biso Wilson estimate: 48.6 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.038 / Net I/σ(I): 7.83
Reflection shellResolution: 2.24→2.3 Å / Mean I/σ(I) obs: 0.25 / Num. unique obs: 3392 / CC1/2: 0.327 / CC star: 0.702 / Rpim(I) all: 0.942

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→50.39 Å / SU ML: 0.2641 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236 1927 5.37 %
Rwork0.2046 33973 -
obs0.2064 35900 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.75 Å2
Refinement stepCycle: LAST / Resolution: 2.24→50.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5064 0 22 78 5164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015194
X-RAY DIFFRACTIONf_angle_d1.02667052
X-RAY DIFFRACTIONf_chiral_restr0.0484767
X-RAY DIFFRACTIONf_plane_restr0.0092938
X-RAY DIFFRACTIONf_dihedral_angle_d15.65361895
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.566479466457
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.710062780989
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.30.28411300.26772381X-RAY DIFFRACTION100
2.3-2.360.28491330.24872389X-RAY DIFFRACTION100
2.36-2.430.30741250.25132443X-RAY DIFFRACTION99.92
2.43-2.510.26431220.24592380X-RAY DIFFRACTION100
2.51-2.60.2921320.24842424X-RAY DIFFRACTION100
2.6-2.70.32371170.23482430X-RAY DIFFRACTION100
2.7-2.820.30111420.24122410X-RAY DIFFRACTION100
2.82-2.970.25251350.23052414X-RAY DIFFRACTION100
2.97-3.160.24521310.24372420X-RAY DIFFRACTION100
3.16-3.40.26851420.22792423X-RAY DIFFRACTION100
3.4-3.740.23461340.20492449X-RAY DIFFRACTION100
3.74-4.280.22971510.17782433X-RAY DIFFRACTION100
4.29-5.40.19851530.17022441X-RAY DIFFRACTION100
5.4-50.390.2071800.18262536X-RAY DIFFRACTION99.85
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.807360227451.575092079060.4227394503882.292302176410.8245280377050.771012968692-0.1303178731720.2793676677630.219474371302-0.2396461456050.08528096762560.4076724114780.0844356234066-0.1364952976760.05736679900880.3836222234950.0130562724448-0.04901346087730.4523404101570.03064821263120.3987913709235.7353591567534.5346414281-6.15211424089
22.083435949630.7497963614650.1431231901742.760979853750.1354432362051.1347340053-0.1398131572560.189537796118-0.0636528955541-0.1056463633630.1122341121460.206471693230.139219379287-0.08230337110160.03145840639090.402938198591-0.0185093292424-0.01373267162280.460762492219-0.006470741147190.3767510920278.2056118217525.5641280541-6.88849372966
32.00004438818-1.11270918708-4.419632922761.99989018415-3.356216596272.000042688740.2480075534482.796091237460.3473103046121.9712162693-0.0218293150504-5.470680628742.59961292861-3.63427587199-0.1228529546121.031475694520.0598056265155-0.5193935581070.9871447648720.05471127302061.15305596663.4406128086237.8861649737-5.23488278562
41.952309152840.163236084476-0.9076271645591.459111066350.6139791541461.25182386481-0.05070587570610.838800311304-0.447105245296-0.4010237753380.027126785044-0.18339351083-0.102873980928-0.1553855466250.0153734379440.454693969842-0.04271292397990.03601874168060.650402184296-0.1466438652630.415014190154-25.529927513738.7446623134.8813025357
51.732825589810.352166065591-0.3813000987121.181791149431.350505719442.34568588372-0.2446749997290.711854201697-0.729816472602-0.2777759409180.102267158089-0.0983455686240.146595522593-0.2333809436780.05936313908290.404945700634-0.1248267907310.112512405080.633119954936-0.2568215229940.552646572606-27.716423228829.65924456575.39068455127
64.327865761875.147597141632.637644216627.246364986044.227324206152.66533620223-0.184976633959-2.89805054181-1.475943103041.138094594820.729047203387-0.8103181032611.202603037531.72763458517-0.5185668810540.925809507286-0.2922824434770.1081543211631.04450879222-0.4724476178410.972887450476-25.048851086842.75778290983.7035804455
71.844360267530.320584862917-0.6828557297221.130135417540.8496700036012.88282803538-0.2718897610360.429593068225-0.8681272548390.0390466808607-0.11634733050.2235984438620.476267779774-0.5706697391810.2588270095760.441206441417-0.1584502197290.1066190027950.531275046065-0.1493084540410.755514366394-42.424680835425.898994531222.2055760778
82.150180134711.02998547366-0.2272516722922.127942716750.5492405986891.14789295929-0.2828127676350.755977474311-0.701432318578-0.2569850143080.04708594788290.07069572147330.287794011231-0.3998941283020.1662478875510.436476847497-0.1567882110240.09168179823550.658099938473-0.2529534384370.673293749599-43.009775593926.131408867913.2807999322
92.000063974371.999886070862.000083855632.000025584411.999928985591.99992852999-0.1921609383022.740715717461.864441707430.6955951475540.7056278143843.93466619227-3.27111159686-1.46860453081-0.51051994081.25425838027-0.281560669750.683080942390.899818610632-0.1029709365691.53687582247-41.989351072424.914824358726.2835734125
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 21 through 153)AA21 - 1531 - 133
22(chain 'A' and resid 158 through 247)AA158 - 247134 - 223
33(chain 'A' and resid 301 through 301)AD301
44(chain 'B' and resid 21 through 152)BB21 - 1521 - 132
55(chain 'B' and resid 159 through 246)BB159 - 246133 - 220
66(chain 'B' and resid 301 through 301)BE301
77(chain 'C' and resid 21 through 151)CC21 - 1511 - 131
88(chain 'C' and resid 158 through 246)CC158 - 246132 - 220
99(chain 'C' and resid 301 through 301)CF301

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