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- PDB-6we5: Crystal structure of an inorganic pyrophosphatase from Chlamydia ... -

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Basic information

Entry
Database: PDB / ID: 6we5
TitleCrystal structure of an inorganic pyrophosphatase from Chlamydia trachomatis D/UW-3/Cx
ComponentsInorganic pyrophosphatase
KeywordsHYDROLASE / National Institute of Allergy and Infectious Diseases / NIAID / structural genomics / sexually transmitted infections / STI / STD / pyrophosphate phospho-hydrolase / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / cytosol
Similarity search - Function
Inorganic Pyrophosphatase / Inorganic pyrophosphatase / Inorganic pyrophosphatase signature. / Inorganic pyrophosphatase / Inorganic pyrophosphatase superfamily / Inorganic pyrophosphatase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Inorganic pyrophosphatase
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structure of an inorganic pyrophosphatase from Chlamydia trachomatis D/UW-3/Cx.
Authors: Maddy, J. / Staker, B.L. / Subramanian, S. / Abendroth, J. / Edwards, T.E. / Myler, P.J. / Hybiske, K. / Asojo, O.A.
History
DepositionApr 1, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inorganic pyrophosphatase
B: Inorganic pyrophosphatase
C: Inorganic pyrophosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4106
Polymers73,3413
Non-polymers693
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-78 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 121.190, 124.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 4 and (name N or name...
21(chain B and ((resid 4 and (name N or name...
31(chain C and (resid 4 through 71 or resid 73...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRTHRTHR(chain A and ((resid 4 and (name N or name...AA412
12LYSLYSNANA(chain A and ((resid 4 and (name N or name...AA - D3 - 30111
13LYSLYSNANA(chain A and ((resid 4 and (name N or name...AA - D3 - 30111
14LYSLYSNANA(chain A and ((resid 4 and (name N or name...AA - D3 - 30111
15LYSLYSNANA(chain A and ((resid 4 and (name N or name...AA - D3 - 30111
21THRTHRTHRTHR(chain B and ((resid 4 and (name N or name...BB412
22LYSLYSNANA(chain B and ((resid 4 and (name N or name...BB - E3 - 30111
23LYSLYSNANA(chain B and ((resid 4 and (name N or name...BB - E3 - 30111
24LYSLYSNANA(chain B and ((resid 4 and (name N or name...BB - E3 - 30111
25LYSLYSNANA(chain B and ((resid 4 and (name N or name...BB - E3 - 30111
31THRTHRTYRTYR(chain C and (resid 4 through 71 or resid 73...CC4 - 7112 - 79
32GLYGLYGLYGLY(chain C and (resid 4 through 71 or resid 73...CC73 - 8181 - 89
33GLNGLNGLNGLN(chain C and (resid 4 through 71 or resid 73...CC8290
34THRTHRNANA(chain C and (resid 4 through 71 or resid 73...CC - F4 - 30112
35THRTHRNANA(chain C and (resid 4 through 71 or resid 73...CC - F4 - 30112
36THRTHRNANA(chain C and (resid 4 through 71 or resid 73...CC - F4 - 30112
37THRTHRNANA(chain C and (resid 4 through 71 or resid 73...CC - F4 - 30112

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Components

#1: Protein Inorganic pyrophosphatase / Pyrophosphate phospho-hydrolase / PPase


Mass: 24446.893 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (strain D/UW-3/Cx) (bacteria)
Strain: D/UW-3/Cx / Gene: ppa, CT_772 / Production host: Escherichia coli (E. coli) / References: UniProt: O84777, inorganic diphosphatase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.98 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: ChtrB.01427.a.B1.PW38676 at 31 mg/mL with 3 mM inorganic pyrophosphate against MCSG-1 screen condition D9: 02 M NaCl, 0.1 M Tris pH 8.5, 25% PEG 3350 supplemented with 15% ethylene glycol as ...Details: ChtrB.01427.a.B1.PW38676 at 31 mg/mL with 3 mM inorganic pyrophosphate against MCSG-1 screen condition D9: 02 M NaCl, 0.1 M Tris pH 8.5, 25% PEG 3350 supplemented with 15% ethylene glycol as cryo-protectant, unique pick ID abt7-1, crystal tracking ID 311611d9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→44.99 Å / Num. obs: 27864 / % possible obs: 99.3 % / Redundancy: 8.112 % / Biso Wilson estimate: 56.567 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.046 / Χ2: 0.917 / Net I/σ(I): 25.24 / Num. measured all: 226034 / Scaling rejects: 276
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.318.4180.6213.1516920202620100.9260.66199.2
2.31-2.378.4380.4334.4916707200019800.9590.46299
2.37-2.448.3920.3785.1216155194419250.9730.40399
2.44-2.528.3580.3036.4215637188218710.9790.32399.4
2.52-2.68.3590.2627.4515146182618120.9840.27999.2
2.6-2.698.2960.1959.7814617177517620.990.20899.3
2.69-2.798.2660.16811.4414035170916980.9930.17999.4
2.79-2.98.1850.11716.4813514166016510.9960.12599.5
2.9-3.038.1280.0920.8112834158715790.9970.09699.5
3.03-3.188.0440.06627.3712187152515150.9980.07199.3
3.18-3.357.9280.05332.9611385144514360.9990.05799.4
3.35-3.567.8820.04340.7110814138213720.9990.04699.3
3.56-3.87.8420.03647.3410045129312810.9990.03899.1
3.8-4.117.8550.03153.379395120511960.9990.03399.3
4.11-4.57.7870.02758.2987761133112710.02999.5
4.5-5.037.8440.02560.1878601006100210.02799.6
5.03-5.817.8780.02559.66709090590010.02699.4
5.81-7.127.7090.02360.84599077877710.02599.9
7.12-10.067.4530.02162.6462162062010.022100
10.06-44.996.5890.02159.9523063673500.9990.02295.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1-3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ls0

5ls0


Resolution: 2.25→44.99 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.49
RfactorNum. reflection% reflection
Rfree0.228 2028 7.29 %
Rwork0.1808 --
obs0.1842 27834 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 133.75 Å2 / Biso mean: 61.5474 Å2 / Biso min: 30.32 Å2
Refinement stepCycle: final / Resolution: 2.25→44.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 3 65 4762
Biso mean--69.55 53.05 -
Num. residues----618
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2759X-RAY DIFFRACTION6.65TORSIONAL
12B2759X-RAY DIFFRACTION6.65TORSIONAL
13C2759X-RAY DIFFRACTION6.65TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.310.37411560.27531787194399
2.31-2.370.32521450.26761795194099
2.37-2.440.34051570.26461819197699
2.44-2.520.33991450.24511814195999
2.52-2.610.29341570.24241813197099
2.61-2.710.25841310.22811838196999
2.71-2.830.29411450.23221819196499
2.83-2.980.28751310.22171863199499
2.98-3.170.26421460.21421826197299
3.17-3.420.26871620.20451839200199
3.42-3.760.21481060.17491880198699
3.76-4.30.19351290.14651885201499
4.3-5.420.17151610.136118702031100
5.42-44.990.1921570.15761958211599
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)
14.3847-0.728-1.41412.62541.02093.22190.00261.1002-0.1336-0.3434-0.27450.31060.2807-0.96720.1440.4326-0.1222-0.11150.854-0.00980.419914.706-1.374812.3709
24.6506-0.63680.02261.70710.89715.7951-0.052-0.25710.09820.09030.2335-0.2060.3097-0.0962-0.0010.3714-0.0924-0.0430.3497-0.01760.343125.6674-4.533424.9251
31.41950.90711.58532.11491.99632.4504-0.695-0.687-0.82950.33740.51180.18680.4429-0.46160.10110.5411-0.15830.03570.71610.1040.446217.183-5.150231.0876
43.19090.8396-0.02282.0708-0.62481.6559-0.22710.1381-0.6731-0.06410.0253-0.0130.5304-0.49780.21050.6754-0.20450.03640.5556-0.02230.474423.7275-15.703620.4422
51.5307-0.4797-0.04320.3033-0.08880.0689-0.1045-1.1075-1.15840.68510.320.66560.64450.04010.18090.9504-0.24410.09630.62790.05880.797918.7254-23.669219.8262
63.9841-0.91750.25282.18890.20152.3575-0.12910.0889-0.23310.10350.06970.2010.6432-0.4675-0.00370.4836-0.1422-0.00670.3729-0.00650.37128.1137-9.647517.2503
74.7694-0.93871.00162.550.35340.35340.06580.7423-0.2004-1.0101-0.1431-0.3915-0.02690.236-0.00890.7231-0.07840.02330.5367-0.03190.451436.7157-7.24597.7058
82.1739-0.29351.6450.99431.95946.10470.3112-0.2681-0.2753-0.43410.10880.2091.2966-0.0808-0.35820.7489-0.1216-0.0060.313-0.01140.530434.6449-20.991125.938
94.5768-0.7111-2.26461.61910.3873.60290.07690.5427-0.35720.3779-0.46920.65291.4032-2.18410.32310.7963-0.44040.04711.0142-0.20810.587415.7085-15.020110.4247
103.36771.24950.61732.3271-0.6552.86420.14080.0340.2021-0.1826-0.08340.4798-0.4732-0.9578-0.03910.40690.1789-0.03130.6380.010.401318.308116.986122.4071
110.1090.2068-0.44430.5921-0.9523.2504-0.56980.10570.3322-0.46620.2929-0.1148-0.1252-0.2950.21430.40190.00830.01950.63650.03130.399222.11396.731613.6334
120.79420.7619-0.61261.13050.31792.430.07940.4107-0.019-0.3154-0.01270.295-0.6423-0.4472-0.03340.49710.1222-0.03920.4780.07770.415628.082217.617215.3265
132.96083.862.82765.03983.66292.8034-0.71470.37770.6308-0.19240.24220.3607-1.6571-0.33110.24471.07590.0854-0.24060.91330.33410.920319.765532.79425.1755
144.11270.92230.17663.3963-1.39254.8458-0.01290.35610.2906-0.83250.0718-0.0853-0.431-0.67690.06260.64420.14690.0630.43950.04650.454726.417621.746116.3905
150.82120.68040.40820.59710.45470.4768-0.16470.25890.5733-0.61630.11750.3573-0.9013-0.79720.18450.74160.2246-0.04960.52320.07120.55325.10826.726720.7668
163.55380.64350.87443.1925-3.16685.14260.0376-0.04770.6029-0.24170.03180.0268-1.784-0.30460.12220.81460.1572-0.02320.35240.02460.565529.248128.776521.3054
172.3869-0.10780.91132.5210.36380.9396-0.06360.54170.3689-0.34730.09650.0315-0.8639-0.3729-0.16610.6012-0.01210.02460.44860.08270.474740.165920.790511.1494
184.1585-1.6659-1.01831.79750.64951.3005-0.30750.48370.63240.31540.1787-0.3371-0.51890.1317-0.2250.9711-0.07460.01110.58620.13540.537936.091827.11475.4487
192.8754-0.2219-3.42955.22750.51214.1057-0.17960.8948-0.0597-0.7748-0.02810.552-0.7042-1.4734-0.04350.82390.5405-0.19150.44950.26830.49214.538928.428413.9582
200.0825-0.3856-0.33712.5117-0.07483.9086-0.17330.1715-0.1701-0.08880.30640.06880.2413-0.9688-0.15630.3135-0.05920.02210.70630.05430.455815.11513.192337.2262
212.21980.7255-2.99631.7346-0.93954.18620.1312-0.53590.48670.0864-0.38330.3013-0.3587-1.03010.02810.38510.1204-0.0420.5068-0.00950.43216.894215.924232.5062
220.86570.8303-0.53981.0464-0.38151.7883-0.0952-0.17060.16470.20560.11350.2271-0.3711-0.86-0.07870.41210.15050.00650.8057-0.03870.454214.613711.859549.3349
232.9278-1.6376-2.743.9091.90258.7971-0.3005-0.023-0.0317-0.03530.21340.16850.0445-0.15130.07850.2824-0.00950.01350.51080.00750.316622.1791.885144.1958
244.1944-0.8685-0.16915.44440.43495.9308-0.2248-0.094-0.2830.24290.19970.47110.1899-0.41660.08370.3055-0.03160.05170.4670.03470.314121.94720.229350.7197
254.20312.4445-0.84874.0628-2.65542.21350.2169-0.39560.68120.8779-0.05690.2682-0.4819-0.1753-0.2340.56940.07560.07470.5504-0.08340.461727.105215.764154.66
261.78910.6814-2.05195.773-0.8074.31040.0740.22910.05730.43240.1611.2644-0.0991-0.705-0.04380.35310.02260.09150.94010.08470.55785.38273.408448.2166
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )A3 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 41 )A25 - 41
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 53 )A42 - 53
4X-RAY DIFFRACTION4chain 'A' and (resid 54 through 84 )A54 - 84
5X-RAY DIFFRACTION5chain 'A' and (resid 85 through 96 )A85 - 96
6X-RAY DIFFRACTION6chain 'A' and (resid 97 through 137 )A97 - 137
7X-RAY DIFFRACTION7chain 'A' and (resid 138 through 153 )A138 - 153
8X-RAY DIFFRACTION8chain 'A' and (resid 154 through 189 )A154 - 189
9X-RAY DIFFRACTION9chain 'A' and (resid 190 through 208 )A190 - 208
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 41 )B3 - 41
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 53 )B42 - 53
12X-RAY DIFFRACTION12chain 'B' and (resid 54 through 73 )B54 - 73
13X-RAY DIFFRACTION13chain 'B' and (resid 74 through 84 )B74 - 84
14X-RAY DIFFRACTION14chain 'B' and (resid 85 through 110 )B85 - 110
15X-RAY DIFFRACTION15chain 'B' and (resid 111 through 124 )B111 - 124
16X-RAY DIFFRACTION16chain 'B' and (resid 125 through 153 )B125 - 153
17X-RAY DIFFRACTION17chain 'B' and (resid 154 through 175 )B154 - 175
18X-RAY DIFFRACTION18chain 'B' and (resid 176 through 189 )B176 - 189
19X-RAY DIFFRACTION19chain 'B' and (resid 190 through 208 )B190 - 208
20X-RAY DIFFRACTION20chain 'C' and (resid 4 through 41 )C4 - 41
21X-RAY DIFFRACTION21chain 'C' and (resid 42 through 53 )C42 - 53
22X-RAY DIFFRACTION22chain 'C' and (resid 54 through 96 )C54 - 96
23X-RAY DIFFRACTION23chain 'C' and (resid 97 through 124 )C97 - 124
24X-RAY DIFFRACTION24chain 'C' and (resid 125 through 153 )C125 - 153
25X-RAY DIFFRACTION25chain 'C' and (resid 154 through 189 )C154 - 189
26X-RAY DIFFRACTION26chain 'C' and (resid 190 through 209 )C190 - 209

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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