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- PDB-4omb: Phosphate binding protein -

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Basic information

Entry
Database: PDB / ID: 4omb
TitlePhosphate binding protein
ComponentsPhosphate binding protein
KeywordsTRANSPORT PROTEIN / substrate binding protein
Function / homology
Function and homology information


phosphate ion transport / single-species biofilm formation / phosphate ion binding / periplasmic space / cell adhesion / extracellular region
Similarity search - Function
Phosphate binding protein / : / PBP domain / PBP superfamily domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / : / Phosphate-binding protein PstS / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNeznansky, A. / Opatowsky, Y.
CitationJournal: Faseb J. / Year: 2014
Title: The Pseudomonas aeruginosa phosphate transport protein PstS plays a phosphate-independent role in biofilm formation.
Authors: Neznansky, A. / Blus-Kadosh, I. / Yerushalmi, G. / Banin, E. / Opatowsky, Y.
History
DepositionJan 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphate binding protein
B: Phosphate binding protein
C: Phosphate binding protein
D: Phosphate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,88212
Polymers148,7224
Non-polymers1,1608
Water8,053447
1
A: Phosphate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4703
Polymers37,1801
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4703
Polymers37,1801
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4703
Polymers37,1801
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phosphate binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4703
Polymers37,1801
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.444, 148.092, 216.452
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 25 - 322 / Label seq-ID: 36 - 333

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Phosphate binding protein / PstS


Mass: 37180.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pstS / Plasmid: pET22 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9Z9M3, UniProt: P0DMR4*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Pt
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / Source method: isolated from a natural source / Formula: H2O
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: 1.91 Å3/Da / Density % sol: 35.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: 2.5 M Na Malonate, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9508 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 31, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9508 Å / Relative weight: 1
ReflectionResolution: 1.49→122.22 Å / Num. all: 183396 / Num. obs: 186078 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Biso Wilson estimate: 21.08 Å2 / Rmerge(I) obs: 0.1466 / Rsym value: 0.1523 / Net I/σ(I): 11.89
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.49-1.59191
1.6-1.69199
1.7-1.831100
1.84-21100
2.01-2.241100
2.25-2.591100

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Processing

Software
NameVersionClassification
EDNAdata collection
BALBESphasing
REFMAC5.8.0049refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TWY

1twy


Resolution: 1.5→122.2 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 5.033 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21571 9126 5 %RANDOM
Rwork0.19016 ---
obs0.19144 173385 98.34 %-
all-182512 --
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.52 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å2-0 Å2-0 Å2
2--1.16 Å2-0 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.5→122.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9024 0 24 447 9495
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029228
X-RAY DIFFRACTIONr_bond_other_d0.0080.028912
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.97912524
X-RAY DIFFRACTIONr_angle_other_deg1.385320604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95451188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16625.824364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.867151564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7111524
X-RAY DIFFRACTIONr_chiral_restr0.0890.21400
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110512
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021936
X-RAY DIFFRACTIONr_mcbond_it3.4951.3644764
X-RAY DIFFRACTIONr_mcbond_other3.4961.3644763
X-RAY DIFFRACTIONr_mcangle_it4.4552.0365948
X-RAY DIFFRACTIONr_mcangle_other4.4552.0375949
X-RAY DIFFRACTIONr_scbond_it8.0522.1114464
X-RAY DIFFRACTIONr_scbond_other8.0652.1134449
X-RAY DIFFRACTIONr_scangle_other112.7876553
X-RAY DIFFRACTIONr_long_range_B_refined12.2712.30510466
X-RAY DIFFRACTIONr_long_range_B_other12.30712.05510337
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: INTERATOMIC DISTANCE / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A185190.07
12B185190.07
21A181760.09
22C181760.09
31A182230.08
32D182230.08
41B181180.09
42C181180.09
51B181730.09
52D181730.09
61C183820.08
62D183820.08
LS refinement shellResolution: 1.5→1.535 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 537 -
Rwork0.492 10210 -
obs--79.11 %
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)
11.1712-0.519-0.31981.36750.22090.70850.00820.0384-0.0003-0.0190.0112-0.0388-0.00180.0477-0.01940.1282-0.0144-0.01860.01020.0020.0086-10.878-33.16421.934
21.3565-0.79710.12372.1180.06230.63510.06560.154-0.0721-0.1354-0.04030.10220.0304-0.0361-0.02530.157-0.00290.00120.0239-0.00470.0311-6.5236.678-5.584
30.80460.5155-0.50751.9754-1.16761.830.0682-0.10570.05640.2749-0.02930.0961-0.10520.0482-0.03890.21930.010.0050.0159-0.00750.01232.45416.26226.96
41.3074-0.47060.48821.7293-0.78072.2770.07190.28690.0592-0.2813-0.076-0.01810.035-0.09050.0040.24070.00210.01140.1289-0.01870.027-15.41530.2754.319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 322
2X-RAY DIFFRACTION2B25 - 322
3X-RAY DIFFRACTION3C25 - 322
4X-RAY DIFFRACTION4D25 - 322

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