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- PDB-5ihp: Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Myc... -

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Basic information

Entry
Database: PDB / ID: 5ihp
TitleCrystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis with bound ADP and Magnesium
ComponentsCobyrinic Acid a,c-diamide synthase
KeywordsLIGASE / SSGCID / COBYRINIC ACID A / C-DIAMIDE SYNTHASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


nucleotide binding / metal ion binding
Similarity search - Function
: / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cobyrinic Acid a,c-diamide synthase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis with bound ATP analog and Magnesium
Authors: Davies, D.R. / Horanyi, P.S. / Abendroth, J.A. / SSGCID
History
DepositionFeb 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references / Structure summary
Revision 1.2Jul 6, 2016Group: Structure summary
Revision 1.3Sep 27, 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 / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cobyrinic Acid a,c-diamide synthase
B: Cobyrinic Acid a,c-diamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7256
Polymers58,8222
Non-polymers9034
Water4,990277
1
A: Cobyrinic Acid a,c-diamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8623
Polymers29,4111
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cobyrinic Acid a,c-diamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8623
Polymers29,4111
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.750, 88.750, 120.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1235-

HOH

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Components

#1: Protein Cobyrinic Acid a,c-diamide synthase


Mass: 29410.924 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_1927 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QTQ5
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#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.: 277 / 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: 2.01 Å3/Da / Density % sol: 38.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: EBS INTERNAL TRACKING NUMBER 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH JCSG SCREEN CONDITION F3: 20% (V/V) MPD, 100 MM TRIS PH 8.0; 3 DAY SOAK WITH 5 ...Details: EBS INTERNAL TRACKING NUMBER 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH JCSG SCREEN CONDITION F3: 20% (V/V) MPD, 100 MM TRIS PH 8.0; 3 DAY SOAK WITH 5 MM ADP + 5 MM MGCL2; 20% ETHYLENE GLYCOL CRYOPROTECTANT
PH range: 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→42 Å / Num. obs: 41651 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.07 % / Biso Wilson estimate: 30.38 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 29.11
Reflection shellResolution: 1.85→1.9 Å / Rmerge(I) obs: 0.542 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX(DEV_2299: ???)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PFS

4pfs


Resolution: 1.85→41.63 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.203 1886 4.53 %
Rwork0.172 --
obs-41649 99.97 %
Displacement parametersBiso mean: 28.94 Å2
Refinement stepCycle: LAST / Resolution: 1.85→41.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3619 0 56 277 3952

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