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- PDB-4mpo: 1.90 A resolution structure of CT771 from Chlamydia trachomatis B... -

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Basic information

Entry
Database: PDB / ID: 4mpo
Title1.90 A resolution structure of CT771 from Chlamydia trachomatis Bound to Hydrolyzed Ap4A Products
ComponentsCT771
KeywordsHYDROLASE / hypothetical protein / Nudix / Ap4A / binary complex
Function / homology
Function and homology information


AMP biosynthetic process / bis(5'-nucleosyl)-tetraphosphatase (asymmetrical) activity / ATP biosynthetic process / hydrolase activity / nucleotide binding / metal ion binding
Similarity search - Function
Bis(5'-nucleosyl)-tetraphosphatase / : / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain ...Bis(5'-nucleosyl)-tetraphosphatase / : / NUDIX hydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / Nucleoside Triphosphate Pyrophosphohydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PHOSPHATE ION / Bis(5'-nucleosyl)-tetraphosphatase [asymmetrical] / Nudix hydrolase domain-containing protein
Similarity search - Component
Biological speciesChlamydia trachomatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBarta, M.L. / Lovell, S. / Battaile, K.P. / Hefty, P.S.
CitationJournal: Biochemistry / Year: 2014
Title: Chlamydia trachomatis CT771 (nudH) Is an Asymmetric Ap4A Hydrolase.
Authors: Barta, M.L. / Lovell, S. / Sinclair, A.N. / Battaile, K.P. / Hefty, P.S.
History
DepositionSep 13, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 15, 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_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_alt_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.pdbx_ptnr1_label_alt_id / _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_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: CT771
B: CT771
C: CT771
D: CT771
E: CT771
F: CT771
G: CT771
H: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,71456
Polymers141,3438
Non-polymers4,37148
Water5,891327
1
A: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2187
Polymers17,6681
Non-polymers5516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2187
Polymers17,6681
Non-polymers5516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2077
Polymers17,6681
Non-polymers5396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2187
Polymers17,6681
Non-polymers5516
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2438
Polymers17,6681
Non-polymers5757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1836
Polymers17,6681
Non-polymers5155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1836
Polymers17,6681
Non-polymers5155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: CT771
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2438
Polymers17,6681
Non-polymers5757
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)182.528, 102.813, 65.363
Angle α, β, γ (deg.)90.00, 94.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
CT771


Mass: 17667.928 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydia trachomatis (bacteria) / Strain: 434/Bu / Gene: CTL0140 / Plasmid: pTBSG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B0B8Z7, UniProt: A0A0H3MCJ9*PLUS, Hydrolases

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Non-polymers , 5 types, 375 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#5: Chemical...
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 43.17 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M magnesium chloride, 0.1 M Tris-HCl, pH 8.5, 25% w/v PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→91.038 Å / Num. all: 94728 / Num. obs: 93781 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 34.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 2.1 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
Aimless0.1.29data scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ILQ

4ilq


Resolution: 1.9→39.627 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.27 / σ(F): 1.33 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2501 4696 5.01 %
Rwork0.2035 --
obs0.2059 93746 98.98 %
all-94712 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.0155 Å2
Refinement stepCycle: LAST / Resolution: 1.9→39.627 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9018 0 256 327 9601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159674
X-RAY DIFFRACTIONf_angle_d0.87412973
X-RAY DIFFRACTIONf_dihedral_angle_d14.853228
X-RAY DIFFRACTIONf_chiral_restr0.0511376
X-RAY DIFFRACTIONf_plane_restr0.0061669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.35821300.30383022X-RAY DIFFRACTION100
1.9216-1.94420.34111360.29652972X-RAY DIFFRACTION99
1.9442-1.96790.33151430.2932991X-RAY DIFFRACTION100
1.9679-1.99280.351620.28432964X-RAY DIFFRACTION100
1.9928-2.01910.33161570.27332985X-RAY DIFFRACTION100
2.0191-2.04670.32471560.26912996X-RAY DIFFRACTION100
2.0467-2.07590.35351470.26942982X-RAY DIFFRACTION100
2.0759-2.10690.33611850.2613002X-RAY DIFFRACTION100
2.1069-2.13990.28221750.2562927X-RAY DIFFRACTION100
2.1399-2.17490.29071710.24252975X-RAY DIFFRACTION100
2.1749-2.21240.27011580.24382983X-RAY DIFFRACTION100
2.2124-2.25270.29051480.23443010X-RAY DIFFRACTION100
2.2527-2.2960.29221530.22932929X-RAY DIFFRACTION99
2.296-2.34280.31711570.23453025X-RAY DIFFRACTION100
2.3428-2.39380.30581610.23892987X-RAY DIFFRACTION100
2.3938-2.44950.28271470.23612989X-RAY DIFFRACTION100
2.4495-2.51070.28211640.23132962X-RAY DIFFRACTION100
2.5107-2.57860.28021480.23252991X-RAY DIFFRACTION100
2.5786-2.65440.30281710.2412983X-RAY DIFFRACTION100
2.6544-2.74010.28931530.23572972X-RAY DIFFRACTION99
2.7401-2.8380.31211510.23493031X-RAY DIFFRACTION100
2.838-2.95160.27411660.22892919X-RAY DIFFRACTION99
2.9516-3.08590.2751630.22172977X-RAY DIFFRACTION99
3.0859-3.24850.27341540.22632948X-RAY DIFFRACTION98
3.2485-3.45190.26541590.19032928X-RAY DIFFRACTION98
3.4519-3.71830.22141480.17962918X-RAY DIFFRACTION97
3.7183-4.09210.19561700.16372897X-RAY DIFFRACTION96
4.0921-4.68340.1731690.13922908X-RAY DIFFRACTION97
4.6834-5.89750.16921440.15022950X-RAY DIFFRACTION97
5.8975-39.63550.24091500.1882927X-RAY DIFFRACTION95

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