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- PDB-5ip0: PHA Binding Protein PhaP (Phasin) -

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Basic information

Entry
Database: PDB / ID: 5ip0
TitlePHA Binding Protein PhaP (Phasin)
ComponentsPHA granule-associated protein
KeywordsSTRUCTURAL PROTEIN / PHB / Polyhydroxyalkanoates / PhaP / Biosurfactant / Amphiphilicity / Point Mutation / Emulsification
Function / homologyPhasin, subfamily 3 / Phasin / Phasin protein / : / PHA granule-associated protein
Function and homology information
Biological speciesAeromonas hydrophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsChen, G.Q. / Wang, X.Q. / Zhao, H.Y.
Funding support China, 1items
OrganizationGrant numberCountry
the State Basic Science Foundation 9732012CB725201 China
CitationJournal: Sci Rep / Year: 2016
Title: Structural Insights on PHA Binding Protein PhaP from Aeromonas hydrophila
Authors: Zhao, H. / Wei, H. / Liu, X. / Yao, Z. / Xu, M. / Wei, D. / Wang, J. / Wang, X. / Chen, G.Q.
History
DepositionMar 9, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHA granule-associated protein
B: PHA granule-associated protein
C: PHA granule-associated protein
D: PHA granule-associated protein
E: PHA granule-associated protein
F: PHA granule-associated protein
G: PHA granule-associated protein
H: PHA granule-associated protein
I: PHA granule-associated protein
J: PHA granule-associated protein
K: PHA granule-associated protein
L: PHA granule-associated protein
M: PHA granule-associated protein
N: PHA granule-associated protein
O: PHA granule-associated protein
P: PHA granule-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,76145
Polymers202,50116
Non-polymers3,26029
Water0
1
A: PHA granule-associated protein
B: PHA granule-associated protein
C: PHA granule-associated protein
D: PHA granule-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,74914
Polymers50,6254
Non-polymers1,12410
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-120 kcal/mol
Surface area19620 Å2
MethodPISA
2
E: PHA granule-associated protein
F: PHA granule-associated protein
G: PHA granule-associated protein
H: PHA granule-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,41211
Polymers50,6254
Non-polymers7877
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12270 Å2
ΔGint-121 kcal/mol
Surface area19700 Å2
MethodPISA
3
I: PHA granule-associated protein
J: PHA granule-associated protein
K: PHA granule-associated protein
L: PHA granule-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,52512
Polymers50,6254
Non-polymers8998
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-118 kcal/mol
Surface area19620 Å2
MethodPISA
4
M: PHA granule-associated protein
N: PHA granule-associated protein
O: PHA granule-associated protein
P: PHA granule-associated protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0758
Polymers50,6254
Non-polymers4504
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12230 Å2
ΔGint-119 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.785, 174.141, 198.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
PHA granule-associated protein / Putative regulative protein


Mass: 12656.328 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeromonas hydrophila (bacteria) / Gene: phaP / Production host: Escherichia coli (E. coli) / References: UniProt: O32470
#2: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: Cd

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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: 2.82 Å3/Da / Density % sol: 56.33 %
Description: (Ta6Br12)2+-SAD method was used for the structure determination.
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.5M sodium acetate trihydrate, 0.15M cadmium sulfate hydrate, 0.1M HEPES buffer (pH 7.5)
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: MACSCIENCE / Wavelength: 0.9796 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 13, 2014
RadiationMonochromator: Ta cluster / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 43885 / % possible obs: 99.7 %

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 3→46.852 Å / SU ML: 0.51 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 34.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2947 2187 4.98 %
Rwork0.2265 --
obs0.2298 43883 95.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→46.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12000 0 29 0 12029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912064
X-RAY DIFFRACTIONf_angle_d1.20416284
X-RAY DIFFRACTIONf_dihedral_angle_d16.1837492
X-RAY DIFFRACTIONf_chiral_restr0.0571996
X-RAY DIFFRACTIONf_plane_restr0.0072128
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0001-3.06530.47411370.36382541X-RAY DIFFRACTION94
3.0653-3.13660.4041460.34852567X-RAY DIFFRACTION95
3.1366-3.2150.42591410.31732576X-RAY DIFFRACTION95
3.215-3.30190.32381400.29592567X-RAY DIFFRACTION95
3.3019-3.39910.34011340.27882550X-RAY DIFFRACTION95
3.3991-3.50870.30441390.25572568X-RAY DIFFRACTION95
3.5087-3.63410.3341230.21812610X-RAY DIFFRACTION95
3.6341-3.77960.27341350.20792597X-RAY DIFFRACTION95
3.7796-3.95150.26761410.19552542X-RAY DIFFRACTION95
3.9515-4.15970.2451180.19412622X-RAY DIFFRACTION95
4.1597-4.42010.27171540.19372565X-RAY DIFFRACTION95
4.4201-4.76110.27411360.18912602X-RAY DIFFRACTION95
4.7611-5.23970.27931470.20642614X-RAY DIFFRACTION95
5.2397-5.99650.32481280.25422746X-RAY DIFFRACTION99
5.9965-7.54990.33441470.23862756X-RAY DIFFRACTION99
7.5499-46.85790.24181210.20682675X-RAY DIFFRACTION92
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)
11.3682-0.0178-0.83020.5672-0.19972.76490.09270.0020.08880.0127-0.08820.0654-0.038-0.21030.00020.8722-0.10630.0920.78970.03690.862-54.7094-24.3504104.5066
23.0337-0.6414-0.90932.0295-0.20381.19610.02860.20010.0856-0.2244-0.0113-0.0881-0.0841-0.1007-00.7428-0.02320.0690.6956-0.03930.7035-88.8414-33.071127.288
32.4367-0.811.0771.8931-0.31841.6043-0.02180.2721-0.3676-0.33740.01220.05260.0550.1290.00010.7512-0.02050.03220.65060.03990.773-20.1615-15.9168127.4627
41.67460.14430.43932.5161-0.06332.55680.0403-0.6095-0.13960.495-0.0363-0.2456-0.05250.0878-0.00110.863-0.0368-0.07140.90630.08990.7653-21.297718.4938149.4837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B or chain C or chain D
2X-RAY DIFFRACTION2chain E or chain F or chain G or chain H
3X-RAY DIFFRACTION3chain I or chain J or chain K or chain L
4X-RAY DIFFRACTION4chain M or chain N or chain O or chain P

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