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- PDB-9jq0: Acid phosphatase KpAP mutant - E104G -

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Basic information

Entry
Database: PDB / ID: 9jq0
TitleAcid phosphatase KpAP mutant - E104G
ComponentsAcid phosphatase
KeywordsHYDROLASE / Acid phosphatase / E104G mutant
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
PHOSPHATE ION / Acid phosphatase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWang, X.L. / Linghu, K. / Xu, K.J.
Funding support China, 2items
OrganizationGrant numberCountry
Other government2019YFA0904900 China
Other governmentBK20202002 China
CitationJournal: To Be Published
Title: Structure of E104G mutant of Acid phosphatase KpAP at 1.93 A resolution
Authors: Wang, X.L. / Linghu, K. / Xu, K.J. / Zhou, J.W.
History
DepositionSep 27, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,25111
Polymers25,3091
Non-polymers94110
Water2,576143
1
A: Acid phosphatase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)157,50366
Polymers151,8576
Non-polymers5,64660
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_554-y,-x,-z-1/21
crystal symmetry operation11_654-x+y+1,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area27120 Å2
ΔGint-442 kcal/mol
Surface area49300 Å2
MethodPISA
2
A: Acid phosphatase
hetero molecules

A: Acid phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,50122
Polymers50,6192
Non-polymers1,88220
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area7200 Å2
ΔGint-115 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.710, 124.710, 97.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-517-

HOH

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Components

#1: Protein Acid phosphatase


Mass: 25309.475 Da / Num. of mol.: 1 / Mutation: E122G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: KPK_3238 / Production host: Escherichia coli (E. coli) / References: UniProt: B5XS64, acid phosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 4.31 Å3/Da / Density % sol: 71.49 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Ammonium acetate, 0.1 M BIS-TRIS, 45% (v/v) (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 17, 2024
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.93→47.21 Å / Num. obs: 34115 / % possible obs: 100 % / Redundancy: 30.3 % / Rmerge(I) obs: 0.192 / Net I/σ(I): 15.8
Reflection shellResolution: 1.93→1.97 Å / Rmerge(I) obs: 1.8 / Num. unique obs: 2242 / Rpim(I) all: 0.503

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Processing

Software
NameVersionClassification
HKL-30007.21data scaling
REFMAC5.8.0123refinement
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→47.21 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.63 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19772 1765 5.2 %RANDOM
Rwork0.17817 ---
obs0.17917 32342 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20.39 Å20 Å2
2--0.77 Å2-0 Å2
3----2.51 Å2
Refinement stepCycle: 1 / Resolution: 1.93→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1772 0 53 143 1968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0191898
X-RAY DIFFRACTIONr_bond_other_d0.0010.021770
X-RAY DIFFRACTIONr_angle_refined_deg1.5891.9752587
X-RAY DIFFRACTIONr_angle_other_deg0.68434084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7785244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91624.65186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.74415305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6391511
X-RAY DIFFRACTIONr_chiral_restr0.050.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212163
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02416
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.432.215941
X-RAY DIFFRACTIONr_mcbond_other0.4312.213940
X-RAY DIFFRACTIONr_mcangle_it0.7913.3171178
X-RAY DIFFRACTIONr_mcangle_other0.793.3191179
X-RAY DIFFRACTIONr_scbond_it0.4932.473957
X-RAY DIFFRACTIONr_scbond_other0.4922.473957
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7053.6691403
X-RAY DIFFRACTIONr_long_range_B_refined7.45629.6862341
X-RAY DIFFRACTIONr_long_range_B_other7.00128.3982274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.93→1.978 Å
RfactorNum. reflection% reflection
Rfree0.257 117 -
Rwork0.273 2357 -
obs--99.84 %
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)
112.30291.5242-2.96413.3092-0.95656.0157-0.12090.263-0.6881-0.17060.0061-0.48860.57780.36820.11480.2126-0.0125-0.03670.07810.03960.214841.8973-68.5088-12.3537
21.821.2789-0.11961.3369-0.06480.59580.0748-0.0128-0.0780.1051-0.0090.02540.0957-0.077-0.06580.0282-0.0162-0.00920.01350.01390.031146.7532-51.4764-15.8027
32.1850.1369-0.29421.0089-0.03081.11810.1162-0.18770.05310.1865-0.03840.08750.0289-0.1891-0.07780.0561-0.04270.00710.08160.01630.016733.2892-48.9365-8.5488
46.8486-2.8471-1.06784.18053.2442.7844-0.1092-0.8228-0.08980.74930.00090.14130.6678-0.18910.10830.2014-0.07110.02160.14750.01550.031452.6751-44.7848-4.2306
53.47831.09360.41571.29610.73661.08160.132-0.16150.12010.1609-0.02850.00760.0391-0.1445-0.10360.0398-0.00740.00850.05310.01540.020337.162-48.2325-15.229
610.3464-6.1979-1.89612.08351.36945.0732-0.0142-0.19570.07470.1697-0.0530.7581-0.3322-0.49780.06720.0759-0.0485-0.00630.22020.02720.132415.9054-54.0808-14.5577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 11
2X-RAY DIFFRACTION2A12 - 55
3X-RAY DIFFRACTION3A56 - 118
4X-RAY DIFFRACTION4A119 - 137
5X-RAY DIFFRACTION5A138 - 211
6X-RAY DIFFRACTION6A212 - 233

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