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- PDB-5if9: Crystal Structure of Cobyrinic Acid a,c-diamide synthase from Myc... -

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Basic information

Entry
Database: PDB / ID: 5if9
TitleCrystal Structure of Cobyrinic Acid a,c-diamide synthase from Mycobacterium smegmatis with bound ATP analog 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


AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cobyrinic Acid a,c-diamide synthase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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. / Dranow, D.M. / Abendroth, J.A. / SSGCID
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references / Structure summary
Revision 1.2Jul 6, 2016Group: Structure summary
Revision 1.3Jul 13, 2016Group: Data collection
Revision 1.4Sep 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

Downloads & links

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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)59,8196
Polymers58,7582
Non-polymers1,0614
Water7,602422
1
A: Cobyrinic Acid a,c-diamide synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9093
Polymers29,3791
Non-polymers5312
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)29,9093
Polymers29,3791
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.400, 88.400, 120.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 29378.857 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_1927 / Production host: Escherichia coli (E. coli) / References: UniProt: A0QTQ5
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*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 / Water


Mass: 18.015 Da / Num. of mol.: 422 / 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 Å3/Da / Density % sol: 38.5 %
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 AMPPNP + 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: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 44831 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.12 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.12
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 8.18 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 3.73 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2328: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PFS

4pfs


Resolution: 1.8→44.2 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1914 2035 4.54 %
Rwork0.1601 --
obs0.1615 44830 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 64 422 4125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063786
X-RAY DIFFRACTIONf_angle_d0.8315194
X-RAY DIFFRACTIONf_dihedral_angle_d13.3712284
X-RAY DIFFRACTIONf_chiral_restr0.052644
X-RAY DIFFRACTIONf_plane_restr0.004664
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7999-1.84180.21051320.19512809X-RAY DIFFRACTION100
1.8418-1.88780.23741260.18552800X-RAY DIFFRACTION100
1.8878-1.93890.20621380.17322802X-RAY DIFFRACTION100
1.9389-1.99590.22831210.17022823X-RAY DIFFRACTION100
1.9959-2.06040.191490.16682787X-RAY DIFFRACTION100
2.0604-2.1340.20891410.16522815X-RAY DIFFRACTION100
2.134-2.21940.21221380.15932815X-RAY DIFFRACTION100
2.2194-2.32040.20211290.15512834X-RAY DIFFRACTION100
2.3204-2.44280.19891620.16152813X-RAY DIFFRACTION100
2.4428-2.59580.18021410.16332835X-RAY DIFFRACTION100
2.5958-2.79620.18631230.17022863X-RAY DIFFRACTION100
2.7962-3.07750.19951110.1682880X-RAY DIFFRACTION100
3.0775-3.52270.20251380.15452902X-RAY DIFFRACTION100
3.5227-4.43750.17131330.14232937X-RAY DIFFRACTION100
4.4375-44.21330.16721530.15593080X-RAY DIFFRACTION100
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)
11.036-0.04790.0562.40370.06452.75570.0265-0.099-0.19090.1650.0123-0.07490.30940.1189-0.02520.1049-0.0034-0.02270.10840.01110.12921.0090.27747.0828
23.3466-0.8124-0.13513.8817-0.47514.284-0.01-0.2517-0.03980.16540.0435-0.01120.0928-0.0666-0.03850.0905-0.0092-0.00450.14770.00060.074520.73548.279817.5926
33.92670.3809-0.08350.67981.12962.018-0.028-0.05740.3601-0.0090.0562-0.2176-0.11950.2936-0.02520.0965-0.0409-0.02640.18330.02090.156228.190712.518410.1155
41.0525-0.160.24973.07560.57763.20060.0587-0.0386-0.1007-0.1652-0.0080.05010.0150.0646-0.05450.097-0.00570.01020.12510.00080.108122.53626.3461-4.3109
52.55951.93350.65994.94860.76211.88430.02160.1152-0.1028-0.25770.00750.16290.09640.0802-0.03310.13440.03010.00740.1475-0.02360.138922.707-1.0367-9.0678
62.70090.71150.02162.5951-0.29784.0327-0.08080.0647-0.55160.1190.0307-0.39820.72740.50950.07230.25790.0913-0.02340.1882-0.00910.321928.4191-10.9163-1.6061
72222-9.715122.5427-3.1208-2.588311.217-4.14350.02611.57760.1261.59480.8327-0.0790.3950.3239-0.00750.541930.491-9.9353-17.2777
81.91110.72490.541.3322-0.59332.80890.1299-0.24690.0070.1509-0.10310.06640.0165-0.2341-0.01720.1336-0.05940.00480.1994-0.04380.147748.588622.331518.9587
92.05850.86590.03411.37580.39673.19070.1926-0.3216-0.1960.3681-0.22660.09390.3087-0.45010.04250.276-0.18890.01120.32580.00810.181847.677613.321328.593
101.8065-1.362-1.95374.2093.9576.57730.0703-0.3703-0.07550.40010.1169-0.55140.46930.6334-0.19360.252-0.0446-0.07550.21130.06990.239360.920811.381326.53
113.07950.4334-0.10970.894-0.69072.41230.1477-0.17030.00140.0781-0.1907-0.0663-0.10930.02310.03770.1323-0.0532-0.00730.146-0.02990.110557.48323.820517.0959
123.34331.2666-0.58242.04870.19472.85360.013-0.2752-0.4086-0.0815-0.2551-0.6385-0.07210.30620.19760.1401-0.03770.02980.21430.02030.202268.814524.145514.023
134.3172-0.8702-0.18962.5264-0.05752.13990.20.13020.7624-0.3859-0.2193-0.3902-0.55530.09270.05290.2813-0.03130.03290.15050.00660.26358.562934.94379.3483
145.55320.7361.49475.37130.40425.4805-0.012-0.1420.1235-0.0249-0.09930.2535-0.46-0.1440.06430.201-0.0425-0.00710.0756-0.01330.14253.18534.98129.1298
152.6416-0.8607-1.2414.73110.6884.4815-0.1129-0.00640.0607-0.2030.1060.28830.0931-0.22360.00340.1358-0.0515-0.03610.17460.00840.111148.228425.97153.7128
162224.2625.85458.2142-0.0711-3.5832-1.48594.7827-1.2069-0.42353.6326-1.59161.27420.71980.0139-0.09830.7090.25910.357954.263939.0622-0.6598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 60 )
2X-RAY DIFFRACTION2chain 'A' and (resid 61 through 95 )
3X-RAY DIFFRACTION3chain 'A' and (resid 96 through 132 )
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 164 )
5X-RAY DIFFRACTION5chain 'A' and (resid 165 through 242 )
6X-RAY DIFFRACTION6chain 'A' and (resid 243 through 269 )
7X-RAY DIFFRACTION7chain 'A' and (resid 270 through 270 )
8X-RAY DIFFRACTION8chain 'B' and (resid 9 through 60 )
9X-RAY DIFFRACTION9chain 'B' and (resid 61 through 95 )
10X-RAY DIFFRACTION10chain 'B' and (resid 96 through 122 )
11X-RAY DIFFRACTION11chain 'B' and (resid 123 through 164 )
12X-RAY DIFFRACTION12chain 'B' and (resid 165 through 177 )
13X-RAY DIFFRACTION13chain 'B' and (resid 178 through 210 )
14X-RAY DIFFRACTION14chain 'B' and (resid 211 through 242 )
15X-RAY DIFFRACTION15chain 'B' and (resid 243 through 268 )
16X-RAY DIFFRACTION16chain 'B' and (resid 269 through 269 )

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