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- PDB-4h1x: Crystal structure of a phosphate ABC transporter, phosphate-bindi... -

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Basic information

Entry
Database: PDB / ID: 4h1x
TitleCrystal structure of a phosphate ABC transporter, phosphate-binding protein (SP_2084) from Streptococcus pneumoniae TIGR4 at 1.77 A resolution
ComponentsPhosphate-binding protein pstS 2
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Periplasmic binding protein / PF12849 family / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


phosphate ion transport / plasma membrane
Similarity search - Function
PBP superfamily domain / PBP 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
CITRIC ACID / Phosphate-binding protein PstS 2
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.77 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a phosphate ABC transporter, phosphate-binding protein (SP_2084) from Streptococcus pneumoniae TIGR4 at 1.77 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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

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Assembly

Deposited unit
A: Phosphate-binding protein pstS 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4753
Polymers28,2471
Non-polymers2282
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.743, 61.624, 67.227
Angle α, β, γ (deg.)90.000, 120.300, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphate-binding protein pstS 2 / PBP 2


Mass: 28247.100 Da / Num. of mol.: 1 / Fragment: UNP residues 28-291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: ATCC BAA-334 / TIGR4 / Gene: pstS2, SP_2084 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: P0C2M5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 28-291 OF THE TARGET SEQUENCE.

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 1.00M lithium chloride, 30.00% polyethylene glycol 6000, 0.1M citric acid pH 4.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97922,0.91837,0.97883
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979221
20.918371
30.978831
ReflectionResolution: 1.77→29.482 Å / Num. obs: 23737 / % possible obs: 88.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.224 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 11.24
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.77-1.830.3392.274414115188.1
1.83-1.910.2143.383754715187.7
1.91-1.990.1784.459503627179.4
1.99-2.10.1116.583454530188.9
2.1-2.230.0779.483404532193.2
2.23-2.40.06311.282444527192.2
2.4-2.640.05612.677884393189.4
2.64-3.020.03816.671324228185.5
3.02-3.810.0321.582294490190.8
3.81-29.4820.02623.579694470189.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 1.77→29.482 Å / Cor.coef. Fo:Fc: 0.9541 / Cor.coef. Fo:Fc free: 0.9423 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. CITRATE (CIT) AND CHLORIDE ION HAS BEEN MODELED INTO THE STRUCTURE. 3. EIGHT RESIDUES AT THE N-TERMINUS ARE DISORDERED AND ARE MISSING IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.1996 1211 5.1 %RANDOM
Rwork0.169 ---
obs0.1706 23733 94.64 %-
Displacement parametersBiso max: 102.1 Å2 / Biso mean: 22.9065 Å2 / Biso min: 7.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.6461 Å20 Å2-0.1597 Å2
2---0.1822 Å20 Å2
3----0.4639 Å2
Refine analyzeLuzzati coordinate error obs: 0.205 Å
Refinement stepCycle: LAST / Resolution: 1.77→29.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 14 258 2183
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1033SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes319HARMONIC5
X-RAY DIFFRACTIONt_it2064HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion304SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2653SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2064HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2825HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.52
X-RAY DIFFRACTIONt_other_torsion2.69
LS refinement shellResolution: 1.77→1.85 Å / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.3053 131 4.59 %
Rwork0.2381 2725 -
all0.2411 2856 -
obs--94.64 %
Refinement TLS params.Method: refined / Origin x: 22.9599 Å / Origin y: 8.5676 Å / Origin z: 17.4319 Å
111213212223313233
T-0.0155 Å2-0.0158 Å20.0061 Å2--0.0182 Å20.0006 Å2---0.0639 Å2
L0.6809 °20.4396 °20.2074 °2-0.9205 °20.3014 °2--0.3377 °2
S0.0348 Å °0.003 Å °-0.0165 Å °0.0024 Å °-0.0341 Å °-0.0182 Å °0.0104 Å °-0.0306 Å °-0.0008 Å °

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