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- PDB-4jwo: The crystal structure of a possible phosphate binding protein fro... -

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Basic information

Entry
Database: PDB / ID: 4jwo
TitleThe crystal structure of a possible phosphate binding protein from Planctomyces limnophilus DSM 3776
ComponentsPhosphate binding protein
KeywordsPhosphate binding protein / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


phosphate ion transport / phosphate ion binding
Similarity search - Function
PBP superfamily domain / Phosphate binding protein / : / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / DI(HYDROXYETHYL)ETHER / Phosphate-binding protein
Similarity search - Component
Biological speciesPlanctomyces limnophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.601 Å
AuthorsTan, K. / Gu, M. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible phosphate binding protein from Planctomyces limnophilus DSM 3776
Authors: Tan, K. / Gu, M. / Endres, M. / Joachimiak, A.
History
DepositionMar 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5778
Polymers36,9681
Non-polymers6097
Water5,206289
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.158, 87.158, 75.536
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
DetailsExperimentally unknown.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphate binding protein


Mass: 36968.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Planctomyces limnophilus (bacteria) / Strain: DSM 3776 / Gene: Plim_1490 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: D5SW38

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Non-polymers , 5 types, 296 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 2.0M Ammonium Sulfate, 0.1M Sodium Acetate:HCl, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97899 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 21, 2013 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 1.6→28.6 Å / Num. all: 42889 / Num. obs: 42889 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 50.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.633 / Mean I/σ(I) obs: 3.5 / Num. unique all: 2121 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.601→28.529 Å / SU ML: 0.16 / σ(F): 1.38 / Phase error: 19.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1946 2160 5.04 %random
Rwork0.1716 ---
all0.1727 42851 --
obs0.1727 42851 99.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→28.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 36 289 2487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062272
X-RAY DIFFRACTIONf_angle_d1.073078
X-RAY DIFFRACTIONf_dihedral_angle_d13.235840
X-RAY DIFFRACTIONf_chiral_restr0.07349
X-RAY DIFFRACTIONf_plane_restr0.005393
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6006-1.63780.26931480.23552636X-RAY DIFFRACTION98
1.6378-1.67880.22121560.21882676X-RAY DIFFRACTION100
1.6788-1.72410.26361420.21012718X-RAY DIFFRACTION100
1.7241-1.77490.19731490.20352716X-RAY DIFFRACTION100
1.7749-1.83220.23761270.19832705X-RAY DIFFRACTION100
1.8322-1.89760.18921670.19232716X-RAY DIFFRACTION100
1.8976-1.97360.22021490.18782679X-RAY DIFFRACTION100
1.9736-2.06340.19821260.18532740X-RAY DIFFRACTION100
2.0634-2.17210.24541290.17412729X-RAY DIFFRACTION100
2.1721-2.30820.20671290.17522746X-RAY DIFFRACTION100
2.3082-2.48630.21121380.17462715X-RAY DIFFRACTION100
2.4863-2.73630.19941560.1772705X-RAY DIFFRACTION100
2.7363-3.13180.19921650.17852711X-RAY DIFFRACTION100
3.1318-3.94410.17371330.15592761X-RAY DIFFRACTION100
3.9441-28.53370.16051460.14822738X-RAY DIFFRACTION99
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)
12.8824-1.3191-0.45841.2572-0.81692.7279-0.0861-1.09530.35020.39830.231-0.0282-0.213-0.7148-0.06290.23370.06020.02970.64-0.05860.263524.244452.512924.5918
21.3402-0.7289-0.94591.20291.04222.7393-0.00630.0494-0.14350.0605-0.08740.04460.2681-0.03760.12240.0928-0.02560.01480.1464-0.00120.146739.865935.40233.5083
31.2069-0.6120.66333.00180.8692.8055-0.0376-0.0433-0.11270.1281-0.0366-0.0240.01160.03080.0450.0919-0.03140.00090.13350.02590.126543.035338.589310.6043
43.1681-1.033-0.40710.98610.21371.3530.02790.02120.29390.0159-0.0012-0.046-0.2115-0.2624-0.03540.12010.01850.01530.20590.010.168631.279350.41737.5425
53.7237-2.7453-1.41463.78341.37863.4085-0.0497-0.3280.4844-0.03540.0529-0.2111-0.5781-0.1968-0.03880.2380.0502-0.0190.2224-0.04590.225725.929562.113711.209
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 55 through 130 )
2X-RAY DIFFRACTION2chain 'A' and (resid 131 through 194 )
3X-RAY DIFFRACTION3chain 'A' and (resid 195 through 233 )
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 305 )
5X-RAY DIFFRACTION5chain 'A' and (resid 306 through 338 )

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