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- PDB-2c7i: Structure of protein Ta0514, putative lipoate protein ligase from... -

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Basic information

Entry
Database: PDB / ID: 2c7i
TitleStructure of protein Ta0514, putative lipoate protein ligase from T. acidophilum.
ComponentsPUTATIVE LIPOATE PROTEIN LIGASE
KeywordsLIGASE / LIPOYLATION
Function / homology
Function and homology information


lipoate-protein ligase / lipoate-protein ligase activity / lipoic acid binding / protein lipoylation / protein-containing complex / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Lipoyl protein ligase A/B catalytic domain / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Bira Bifunctional Protein; Domain 2 / BirA Bifunctional Protein; domain 2 / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Lipoate-protein ligase A subunit 1
Similarity search - Component
Biological speciesTHERMOPLASMA ACIDOPHILUM (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMcmanus, E. / Perham, R.N. / Luisi, B.F.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of a Putative Lipoate Protein Ligase from Thermoplasma Acidophilum and the Mechanism of Target Selection for Post-Translational Modification.
Authors: Mcmanus, E. / Luisi, B.F. / Perham, R.N.
History
DepositionNov 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PUTATIVE LIPOATE PROTEIN LIGASE
B: PUTATIVE LIPOATE PROTEIN LIGASE
C: PUTATIVE LIPOATE PROTEIN LIGASE
D: PUTATIVE LIPOATE PROTEIN LIGASE


Theoretical massNumber of molelcules
Total (without water)119,6614
Polymers119,6614
Non-polymers00
Water3,387188
1
A: PUTATIVE LIPOATE PROTEIN LIGASE


Theoretical massNumber of molelcules
Total (without water)29,9151
Polymers29,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PUTATIVE LIPOATE PROTEIN LIGASE


Theoretical massNumber of molelcules
Total (without water)29,9151
Polymers29,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PUTATIVE LIPOATE PROTEIN LIGASE


Theoretical massNumber of molelcules
Total (without water)29,9151
Polymers29,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: PUTATIVE LIPOATE PROTEIN LIGASE


Theoretical massNumber of molelcules
Total (without water)29,9151
Polymers29,9151
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)53.230, 118.356, 105.592
Angle α, β, γ (deg.)90.00, 93.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 1 - 256 / Label seq-ID: 1 - 256

Dom-IDEns-IDRefine codeAuth asym-IDLabel asym-ID
113BB
213AA
124CC
224AA
134DD
234AA

NCS ensembles :
ID
1
2
3

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Components

#1: Protein
PUTATIVE LIPOATE PROTEIN LIGASE / LIPOATE-PROTEIN LIGASE A


Mass: 29915.252 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOPLASMA ACIDOPHILUM (acidophilic) / Strain: DSM 1728 / Plasmid: PET 3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HKT1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.11 Å3/Da / Density % sol: 60.13 %
Description: A STRUCTURE OF RELATIVELY POOR QUALITY DERIVED FROM A SELENOMETHIONE CONTAINING PROTEIN CRYSTAL WAS USED AS MODEL IN CONJUNCTION WITH A GOOD QUALITY NATIVE DATA SET TO GIVE THE STRUCTURE FILES DEPOSITED.
Crystal growpH: 6.7 / Details: pH 6.70

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.54
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→19.87 Å / Num. obs: 68335 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 10 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 22
Reflection shellResolution: 2.08→2.17 Å / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6 / % possible all: 72.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SEE REMARK

Resolution: 2.1→19.87 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.866 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS WITH ZERO OCCUPANCY FOR WHICH B-FACTORS HAVE BEEN REFINED.
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3634 5 %RANDOM
Rwork0.208 ---
obs0.21 68335 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å2-0.18 Å2
2---0.23 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7404 0 0 188 7592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217382
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.9489900
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1165960
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55423.617329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51151185
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.051559
X-RAY DIFFRACTIONr_chiral_restr0.0840.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025581
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2990.23454
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.25049
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2340
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3091.54864
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.02227449
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.21832863
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.7974.52448
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B905tight positional0.130.05
2C1663medium positional0.250.5
3D1654medium positional0.230.5
1B834loose positional0.395
1B905tight thermal1.140.5
2C1663medium thermal4.412
3D1654medium thermal3.22
1B834loose thermal3.2910
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 217
Rwork0.243 4216
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)
10.71020.38910.01463.1032-0.15710.5842-0.0312-0.0493-0.05280.0319-0.0302-0.0737-0.0436-0.0220.0613-0.19760.00150.0684-0.1164-0.0125-0.11186.87810.0498.59
21.9392-1.06580.00942.56450.11140.81710.06960.0881-0.1125-0.1143-0.19310.1638-0.1678-0.00890.1235-0.14180.0164-0.0171-0.124-0.0488-0.0912-10.988-13.718-5.18
31.17940.77560.58012.67770.18093.20570.08940.0737-0.01280.25840.0275-0.060.0274-0.0794-0.11680.1088-0.00260.02390.006-0.0393-0.282119.0948.66241.612
41.36850.41381.23922.5282-0.3323.65410.0194-0.0115-0.1318-0.0039-0.039-0.1360.16930.57740.01960.1604-0.03670.04850.07930.0301-0.185317.04711.76743.414
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 256
2X-RAY DIFFRACTION2B1 - 256
3X-RAY DIFFRACTION3C1 - 256
4X-RAY DIFFRACTION4D1 - 257

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