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- PDB-4yr1: Crystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in ... -

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Basic information

Entry
Database: PDB / ID: 4yr1
TitleCrystal Structure of E. Coli Alkaline Phosphatase D101A/D153A in complex with inorganic phosphate
ComponentsAlkaline phosphatase
KeywordsHYDROLASE
Function / homology
Function and homology information


oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / dephosphorylation / protein dephosphorylation / outer membrane-bounded periplasmic space / periplasmic space / magnesium ion binding / zinc ion binding
Similarity search - Function
Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alkaline phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsPeck, A. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM64798 United States
CitationJournal: Elife / Year: 2015
Title: Extensive site-directed mutagenesis reveals interconnected functional units in the Alkaline Phosphatase active site.
Authors: Sunden, F. / Peck, A. / Salzman, J. / Ressl, S. / Herschlag, D.
History
DepositionMar 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkaline phosphatase
B: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,35512
Polymers92,5352
Non-polymers82010
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-199 kcal/mol
Surface area28010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.420, 161.420, 140.051
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A10 - 447
2115B10 - 447

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.86983, -0.493348, -0.001746), (-0.493321, 0.869732, 0.014179), (-0.005476, 0.013195, -0.999898)-0.35829, 0.18754, -35.74955

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Components

#1: Protein Alkaline phosphatase / APase


Mass: 46267.492 Da / Num. of mol.: 2 / Mutation: D101A D153A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: phoA, b0383, JW0374 / Plasmid: pMAL-p2X / Production host: Escherichia coli (E. coli) / Strain (production host): SM547(DE3) / References: UniProt: P00634, alkaline phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 3350, Bis-Tris, ammonium sulfate, glycerol (cryo-protectant)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.24→52.89 Å / Num. obs: 51846 / % possible obs: 100 % / Redundancy: 21.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.438 / Rpim(I) all: 0.096 / Net I/σ(I): 7.8 / Num. measured all: 1117848 / Scaling rejects: 252
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.24-2.3119.73.1351.48703844200.5820.719100
9.25-52.8922.30.05531.3195038760.9990.01299.6

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Processing

Software
NameVersionClassification
REFMACrefmac_5.8.0073refinement
PHASER2.5.6phasing
Aimless0.3.6data scaling
iMOSFLM7.1.1data reduction
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→52.89 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / Matrix type: sparse / WRfactor Rfree: 0.208 / WRfactor Rwork: 0.169 / SU B: 11.297 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.275 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2589 2548 4.9 %RANDOM
Rwork0.2169 49268 --
obs0.219 49268 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.86 Å2 / Biso mean: 37.56 Å2 / Biso min: 19.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20.78 Å20 Å2
2--1.55 Å20 Å2
3----5.04 Å2
Refinement stepCycle: final / Resolution: 2.24→52.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6492 0 48 182 6722
Biso mean--45.42 30.17 -
Num. residues----886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0196740
X-RAY DIFFRACTIONr_bond_other_d0.0010.026380
X-RAY DIFFRACTIONr_angle_refined_deg1.1041.9639121
X-RAY DIFFRACTIONr_angle_other_deg0.725314707
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7855898
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.08525.362276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.217151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5211532
X-RAY DIFFRACTIONr_chiral_restr0.0590.21037
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021440
X-RAY DIFFRACTIONr_mcbond_it1.2193.6913577
X-RAY DIFFRACTIONr_mcbond_other1.2193.693576
X-RAY DIFFRACTIONr_mcangle_it2.0625.5314480
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2558MEDIUM POSITIONAL0.10.5
3738LOOSE POSITIONAL0.365
2558MEDIUM THERMAL1.662
3738LOOSE THERMAL2.0210
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
2.244-2.3020.3781840.38535970.38537811000.356
2.302-2.3650.3681700.36334620.36336321000.331
2.365-2.4340.3971550.34234230.34435781000.315
2.434-2.5080.3341720.3132960.312346999.9710.273
2.508-2.590.3491650.29631960.298336299.970.258
2.59-2.6810.2941600.26531000.26732601000.228
2.681-2.7820.3431600.26229990.26631591000.223
2.782-2.8950.3341640.24728840.25130481000.21
2.895-3.0240.3071330.23427810.23729141000.199
3.024-3.1710.2981330.24226810.24528141000.21
3.171-3.3410.2721190.21425440.21626631000.183
3.341-3.5430.2341310.19423990.19625301000.173
3.543-3.7870.2071190.18522810.18724001000.164
3.787-4.0880.2351210.15921060.163222899.9550.141
4.088-4.4760.1661100.12919670.13120771000.114
4.476-50.143890.12518030.12618921000.109
5-5.7650.213940.14115930.14516871000.123
5.765-7.0390.181920.16513560.16614481000.15
7.039-9.8680.183470.13711010.138115099.8260.131
9.868-52.890.322300.2196980.2237281000.219

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