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- PDB-4qji: Crystal Structure of the C-terminal CTP-binding domain of a Phosp... -

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Basic information

Entry
Database: PDB / ID: 4qji
TitleCrystal Structure of the C-terminal CTP-binding domain of a Phosphopantothenoylcysteine decarboxylase/phosphopantothenate-cysteine ligase with bound CTP from Mycobacterium smegmatis
ComponentsPhosphopantothenate--cysteine ligase
KeywordsLIGASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / DNA / pantothenate metabolism flavoprotein / CTP-binding / pantothenate metablosim
Function / homology
Function and homology information


pantothenate catabolic process / phosphopantothenoylcysteine decarboxylase / phosphopantothenate-cysteine ligase (CTP) / phosphopantothenate--cysteine ligase activity / phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / coenzyme A biosynthetic process / FMN binding / metal ion binding
Similarity search - Function
CoaB-like / Coenzyme A biosynthesis bifunctional protein CoaBC / DNA/pantothenate metabolism flavoprotein, C-terminal / CoaB-like superfamily / DNA/pantothenate metabolism flavoprotein C-terminal domain / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / Coenzyme A biosynthesis bifunctional protein CoaBC
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of the C-terminal CTP-binding domain of a Phosphopantothenoylcysteine decarboxylase/phosphopantothenate-cysteine ligase with bound CTP from Mycobacterium smegmatis
Authors: Dranow, D.M. / Abendroth, J. / Wernimont, A.K. / Edwards, T.E. / Lorimer, D.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 19, 2018Group: Data collection / Structure summary / Category: entity / entity_name_com / struct
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _struct.pdbx_descriptor
Revision 1.3Feb 28, 2024Group: 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.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_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_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: Phosphopantothenate--cysteine ligase
B: Phosphopantothenate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5636
Polymers49,5482
Non-polymers1,0154
Water41423
1
A: Phosphopantothenate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2813
Polymers24,7741
Non-polymers5072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphopantothenate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2813
Polymers24,7741
Non-polymers5072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Phosphopantothenate--cysteine ligase
hetero molecules

B: Phosphopantothenate--cysteine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,5636
Polymers49,5482
Non-polymers1,0154
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565-x,-y+1,z+1/21
Buried area4570 Å2
ΔGint-28 kcal/mol
Surface area19190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.580, 90.580, 109.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: CTP / End label comp-ID: CTP / Auth seq-ID: 184 - 500 / Label seq-ID: 7

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - C
2chain BBB - E
DetailsAUTHORS HAVE INDICATED THAT THE BIOLOGICAL UNIT IS UNKNOWN

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Components

#1: Protein Phosphopantothenate--cysteine ligase / Phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase / Probable coenzyme ...Phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase / Probable coenzyme A biosynthesis bifunctional protein CoaBC


Mass: 24773.990 Da / Num. of mol.: 2 / Fragment: unp residues 186-414
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: coaBC, MSMEG_3054, MSMEI_2978 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QWT2, phosphopantothenate-cysteine ligase (CTP)
#2: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Wiz3/4(f7): 25% PEG-1500, 0.1M MMT Buffer, pH=7.0; protein was incubated with 10mM each CTP and pantothenate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 26, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. all: 14877 / Num. obs: 14512 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 59.41 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.966 / Net I/σ(I): 16.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.65-2.720.492.133952109199.1
2.72-2.790.3762.763815105899
2.79-2.870.2713.743632101699.2
2.87-2.960.2274.633755103099.1
2.96-3.060.1855.43337694399.2
3.06-3.170.1556.85339193898.4
3.17-3.290.1248.48325289798.8
3.29-3.420.09111.57316387898.9
3.42-3.570.06215.43299282598
3.57-3.750.04819.51286879197.5
3.75-3.950.04621.53276975597.8
3.95-4.190.03626.41254270297.5
4.19-4.480.03232.05240465696.2
4.48-4.840.0333.49222060795.9
4.84-5.30.03232.56207657196
5.3-5.930.02935.2187150495.1
5.93-6.840.02636.5165944894.5
6.84-8.380.0245.96137137393.2
8.38-11.850.01659.41103428792.6
11.850.01758.9745514281.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→33.11 Å / SU ML: 0.39 / σ(F): 1.37 / Phase error: 27.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2482 730 5.03 %RANDOM
Rwork0.1924 ---
obs0.1952 14512 97.59 %-
all-15242 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 160.49 Å2 / Biso mean: 63.814 Å2 / Biso min: 26.96 Å2
Refinement stepCycle: LAST / Resolution: 2.65→33.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2999 0 60 23 3082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023103
X-RAY DIFFRACTIONf_angle_d0.7594230
X-RAY DIFFRACTIONf_chiral_restr0.028508
X-RAY DIFFRACTIONf_plane_restr0.003555
X-RAY DIFFRACTIONf_dihedral_angle_d13.661080
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1670X-RAY DIFFRACTION6.996TORSIONAL
12B1670X-RAY DIFFRACTION6.996TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6501-2.85460.31941610.28262776293799
2.8546-3.14170.32851310.26132803293499
3.1417-3.59580.31631620.21892755291799
3.5958-4.52850.21541500.16912742289297
4.5285-33.1130.20291260.16012706283294
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)
11.93560.14170.52462.42270.79253.937-0.01470.062-0.0263-0.02370.02840.0331-0.13340.1861-0.00790.3397-0.0229-0.00640.35090.00950.3561-14.23328.28-1.454
21.72160.216-0.35690.8989-0.73315.3483-0.068-0.02740.05250.21540.03550.0132-0.2846-0.21490.01630.51980.0364-0.0840.35580.00260.4916-27.48548.234-22.029
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 184:412 )A184 - 412
2X-RAY DIFFRACTION2( CHAIN B AND RESID 185:412 )B185 - 412

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