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- PDB-4gd5: X-ray Crystal Structure of a Putative Phosphate ABC Transporter S... -

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Basic information

Entry
Database: PDB / ID: 4gd5
TitleX-ray Crystal Structure of a Putative Phosphate ABC Transporter Substrate-Binding Protein with Bound Phosphate from Clostridium perfringens
ComponentsPhosphate ABC transporter, phosphate-binding protein
KeywordsTRANSPORT PROTEIN / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / phosphate ABC transporter / phosphate-binding protein
Function / homology
Function and homology information


phosphate ion transport / phosphate ion binding / metal ion binding / plasma membrane
Similarity search - Function
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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Phosphate-binding protein / Phosphate-binding protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsBrunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: X-ray Crystal Structure of a Putative Phosphate ABC Transporter Substrate-Binding Protein with Bound Phosphate from Clostridium perfringens
Authors: Brunzelle, J.S. / Wawrzak, Z. / Onopriyenko, O. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases
History
DepositionJul 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2013Group: Other
Revision 1.2Nov 20, 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 ABC transporter, phosphate-binding protein
B: Phosphate ABC transporter, phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,49810
Polymers59,9982
Non-polymers5008
Water12,268681
1
A: Phosphate ABC transporter, phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1654
Polymers29,9991
Non-polymers1663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphate ABC transporter, phosphate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3336
Polymers29,9991
Non-polymers3345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.888, 73.302, 56.415
Angle α, β, γ (deg.)90.00, 102.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phosphate ABC transporter, phosphate-binding protein


Mass: 29998.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: ATCC 13124 / Gene: CPF_0617, pstS / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q0TTH0, UniProt: A0A0H2YSI2*PLUS

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Non-polymers , 5 types, 689 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 1.88 Å3/Da / Density % sol: 34.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 25%PEG 3350, 0.2M NaBr, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2012 / Details: Be Lens
RadiationMonochromator: Single Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 49208 / Num. obs: 49208 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 15.49 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 21.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 3.3 / Num. unique all: 2427 / % possible all: 100

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIXmodel building
BUSTER2.10.0refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→28.07 Å / Cor.coef. Fo:Fc: 0.9604 / Cor.coef. Fo:Fc free: 0.943 / SU R Cruickshank DPI: 0.103 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1857 2349 5.07 %RANDOM
Rwork0.1505 ---
all0.1523 49208 --
obs0.1523 46348 94.6 %-
Displacement parametersBiso mean: 18.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.0328 Å20 Å20.0865 Å2
2---0.8149 Å20 Å2
3----0.2179 Å2
Refine analyzeLuzzati coordinate error obs: 0.165 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 25 681 4376
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013837HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035184HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2.751849SINUSOIDAL2
X-RAY DIFFRACTIONt_omega_torsion3.73
X-RAY DIFFRACTIONt_other_torsion2.75
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2034 128 5.51 %
Rwork0.1743 2193 -
all0.1759 2321 -
obs-2193 94.6 %
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)
10.76210.57680.69730.1839-0.4252.3163-0.01460.2128-0.1977-0.06480.1447-0.04180.05250.2186-0.1301-0.0328-0.013900.014-0.0447-0.0549-10.027742.522423.6267
20.12481.1702-0.501801.78061.965-0.04260.2831-0.1607-0.1350.1178-0.0970.04090.0598-0.07520.0569-0.04650.00640.0913-0.0532-0.0182-4.793244.148722.0796
32.6575-0.1445-0.48791.2319-0.06061.3595-0.0749-0.00830.1456-0.06850.06580.0561-0.04270.09090.0092-0.0232-0.04450.0023-0.0557-0.0056-0.0624-5.901753.421733.5216
42.71320.31060.34642.7626-0.2961.3531-0.1024-0.27910.4079-0.13120.00690.0936-0.1817-0.07030.0955-0.0068-0.00720.013-0.0097-0.0438-0.0133-14.036255.712235.9631
51.22260.11690.3990.8214-0.82991.64570.0202-0.0808-0.0720.0304-0.0384-0.0028-0.06460.05580.0181-0.0155-0.00860.0049-0.01510.0135-0.0314-11.017935.918355.2445
60.2775-1.0837-0.85992.93690.34772.16020.025-0.36650.37040.03210.0361-0.3378-0.26710.2752-0.06110.0181-0.06630.0030.057-0.01630.0145-7.038346.239655.5335
70.7721-0.16980.53880.3118-0.56011.46660.0390.0967-0.1328-0.0874-0.0276-0.00770.13190.1025-0.0114-0.01790.00620.006-0.0246-0.0036-0.0195-11.414933.010746.0506
81.72561.182-1.71651.3354-1.66932.99150.0468-0.01580.10040.00290.1240.1935-0.1338-0.0643-0.1707-0.0263-0.00650.0121-0.060.0273-0.0335-20.214246.075539.6303
90.93530.895-0.8344.8873-0.90221.98890.04450.38580.2627-0.20970.01870.1465-0.38260.0914-0.06320.1208-0.0318-0.01770.01540.0190.0021-11.758254.744620.0995
104.13750.38120.59681.5199-0.57875.47650.07640.0767-0.302-0.066-0.0397-0.00640.1659-0.2369-0.0366-0.0123-0.033-0.023-0.0261-0.0260-21.62341.188627.6523
110.74840.2371-1.93860.9341-0.25361.7895-0.06610.31840.2265-0.16850.03870.01080.0213-0.30920.0274-0.0367-0.01550.00360.060.0384-0.068813.65260.567424.5532
120.89730.0715-2.19411.32440.56650.9303-0.050.11740.1876-0.12640.12370.01640.1408-0.2104-0.07360.0148-0.02050.01630.08990.0479-0.064611.436959.950719.2162
132.9042-0.27530.41231.0480.28010.3442-0.06880.1421-0.225-0.08270.0984-0.0301-0.0061-0.0879-0.02960.0002-0.03650.009-0.0234-0.0147-0.02349.899650.103933.5217
142.79040.4832-0.68282.3935-0.23991.7907-0.101-0.2043-0.3935-0.04740.0682-0.13890.32660.03960.03280.0260.005-0.0059-0.02090.0118-0.002217.546746.398435.5933
151.28350.2546-0.08750.75110.88511.75770.0331-0.09220.03240.0671-0.0334-0.06190.1002-0.00850.0003-0.01430.0006-0.0055-0.0353-0.006-0.035115.403666.742755.2578
161.7382-0.69570.03850.9510.12681.510.01230.0381-0.00140.0389-0.0363-0.05320.0484-0.07340.024-0.00870.00150.0006-0.0214-0.0083-0.029612.291465.997249.0461
172.81340.6239-1.49851.011.95083.7417-0.01870.1073-0.0758-0.03310.1436-0.03390.0296-0.0254-0.1248-0.04760.0067-0.00830.0001-0.04960.019329.906764.692546.3774
181.3642-0.0628-0.49580.6328-1.18330.0768-0.05510.0227-0.1231-0.15980.1003-0.12220.2207-0.0063-0.04520.0428-0.01130.0064-0.0128-0.01680.005117.773950.385232.6788
192.99860.175-0.11871.2905-0.05951.8199-0.05710.40340.0146-0.13320.05-0.20010.13650.090.0071-0.0162-0.01220.03790.04610.0263-0.064722.339256.83621.3381
201.86152.9336-0.80491.4432-1.82447.6092-0.070.08790.5304-0.22740.02490.117-0.15450.12210.0451-0.0448-0.03230.0122-0.0353-0.01560.021825.921363.731431.9836
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|34 - A|59 }A34 - 59
2X-RAY DIFFRACTION2{ A|60 - A|69 }A60 - 69
3X-RAY DIFFRACTION3{ A|70 - A|92 }A70 - 92
4X-RAY DIFFRACTION4{ A|93 - A|108 }A93 - 108
5X-RAY DIFFRACTION5{ A|109 - A|165 }A109 - 165
6X-RAY DIFFRACTION6{ A|166 - A|181 }A166 - 181
7X-RAY DIFFRACTION7{ A|182 - A|224 }A182 - 224
8X-RAY DIFFRACTION8{ A|225 - A|243 }A225 - 243
9X-RAY DIFFRACTION9{ A|244 - A|255 }A244 - 255
10X-RAY DIFFRACTION10{ A|256 - A|276 }A256 - 276
11X-RAY DIFFRACTION11{ B|34 - B|57 }B34 - 57
12X-RAY DIFFRACTION12{ B|58 - B|68 }B58 - 68
13X-RAY DIFFRACTION13{ B|69 - B|92 }B69 - 92
14X-RAY DIFFRACTION14{ B|93 - B|108 }B93 - 108
15X-RAY DIFFRACTION15{ B|109 - B|165 }B109 - 165
16X-RAY DIFFRACTION16{ B|166 - B|215 }B166 - 215
17X-RAY DIFFRACTION17{ B|216 - B|232 }B216 - 232
18X-RAY DIFFRACTION18{ B|233 - B|247 }B233 - 247
19X-RAY DIFFRACTION19{ B|248 - B|266 }B248 - 266
20X-RAY DIFFRACTION20{ B|267 - B|276 }B267 - 276

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