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- PDB-2cgq: a putative acyl carrier protein(Rv0033) from Mycobacterium tuberc... -

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Basic information

Entry
Database: PDB / ID: 2cgq
Titlea putative acyl carrier protein(Rv0033) from Mycobacterium tuberculosis
ComponentsACYL CARRIER PROTEIN ACPA
KeywordsPROTEIN TRANSPORT / RV0033 / ACYL CARRIER PROTEIN / PHOSPHOPANTETHEINE
Function / homology
Function and homology information


fatty acid biosynthetic process
Similarity search - Function
ACP-like / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Acyl carrier protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsMa, Q. / Wilmanns, M.
CitationJournal: To be Published
Title: The Structure of a Putative Acyl Carrier Protein (Rv0033) from Mycobacterium Tuberculosis
Authors: Ma, Q. / Wilmanns, M.
History
DepositionMar 9, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 13, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ACYL CARRIER PROTEIN ACPA


Theoretical massNumber of molelcules
Total (without water)12,7551
Polymers12,7551
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.222, 45.222, 78.152
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein ACYL CARRIER PROTEIN ACPA / ACP / ACYL CARRIER PROTEIN


Mass: 12755.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS / References: UniProt: P71603
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsOWING TO GENE CONSTRUCTION METHOD, SOME FOREIGN RESIDUES ARE INTRODUCED INTO THE N-TERMINAL. ...OWING TO GENE CONSTRUCTION METHOD, SOME FOREIGN RESIDUES ARE INTRODUCED INTO THE N-TERMINAL. RESIDUES WITH POOR ELECTRON DENSITY ARE NOT BUILT INTO THE MODEL.

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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: 1.8 Å3/Da / Density % sol: 31.5 %
Crystal growpH: 6.5
Details: 0.1M BIS-TRIS PH6.5, 0.2M NACL, 25%(W/V)PEG3350, pH 6.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8075
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 23, 2005 / Details: MIRROR
RadiationMonochromator: FOCUSSING SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8075 Å / Relative weight: 1
ReflectionResolution: 1.83→39.16 Å / Num. obs: 8555 / % possible obs: 98.8 % / Redundancy: 6.25 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 35.74
Reflection shellResolution: 1.83→1.95 Å / Redundancy: 5.54 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 9.19 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T8K

1t8k


Resolution: 1.83→39.16 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.464 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.217 829 9.7 %RANDOM
Rwork0.179 ---
obs0.182 7690 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.3 Å20 Å2
2--0.59 Å20 Å2
3----0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.83→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms589 0 0 64 653
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022613
X-RAY DIFFRACTIONr_bond_other_d0.0010.02567
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.941833
X-RAY DIFFRACTIONr_angle_other_deg0.85931312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.286575
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45425.45533
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24215109
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.039154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2101
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02686
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02125
X-RAY DIFFRACTIONr_nbd_refined0.2260.2127
X-RAY DIFFRACTIONr_nbd_other0.1640.2600
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2323
X-RAY DIFFRACTIONr_nbtor_other0.0830.2379
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3620.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.231.5489
X-RAY DIFFRACTIONr_mcbond_other0.3221.5155
X-RAY DIFFRACTIONr_mcangle_it1.4592610
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6253272
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.654.5223
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
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 54 -
Rwork0.276 519 -
obs--98.45 %
Refinement TLS params.Method: refined / Origin x: 12.2581 Å / Origin y: 14.4889 Å / Origin z: 26.1412 Å
111213212223313233
T-0.0127 Å20.0173 Å2-0.0222 Å2--0.0731 Å2-0.0124 Å2---0.0554 Å2
L2.1444 °2-0.8039 °2-0.8057 °2-1.7451 °20.6713 °2--2.3848 °2
S0.1575 Å °0.0886 Å °-0.0983 Å °-0.2522 Å °-0.036 Å °-0.0379 Å °0.0606 Å °-0.0892 Å °-0.1215 Å °

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