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- PDB-3wvq: Structure of ATP grasp protein -

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Basic information

Entry
Database: PDB / ID: 3wvq
TitleStructure of ATP grasp protein
ComponentsPGM1
KeywordsBIOSYNTHETIC PROTEIN / ATP grasp domain / LIGASE
Function / homologyPre ATP-grasp domain / PGM1 C-terminal domain / PGM1 C-terminal domain / Pre ATP-grasp domain / ATP-grasp fold / ATP-grasp fold profile. / ATP binding / metal ion binding / PGM1
Function and homology information
Biological speciesStreptomyces cirratus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.955 Å
AuthorsMatsui, T. / Noike, M. / Ooya, K. / Sasaki, I. / Hamano, Y. / Maruyama, C. / Ishikawa, J. / Satoh, Y. / Ito, H. / Dairi, T. / Morita, H.
CitationJournal: Nat.Chem.Biol. / Year: 2015
Title: A peptide ligase and the ribosome cooperate to synthesize the peptide pheganomycin.
Authors: Noike, M. / Matsui, T. / Ooya, K. / Sasaki, I. / Ohtaki, S. / Hamano, Y. / Maruyama, C. / Ishikawa, J. / Satoh, Y. / Ito, H. / Morita, H. / Dairi, T.
History
DepositionJun 4, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: PGM1
B: PGM1
C: PGM1
D: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,09021
Polymers194,4654
Non-polymers1,62517
Water23,4011299
1
A: PGM1
B: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,99710
Polymers97,2322
Non-polymers7658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: PGM1
D: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,09311
Polymers97,2322
Non-polymers8619
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9044
Polymers48,6161
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0926
Polymers48,6161
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2858
Polymers48,6161
Non-polymers6687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8083
Polymers48,6161
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.660, 86.750, 94.260
Angle α, β, γ (deg.)73.740, 85.930, 68.260
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PGM1


Mass: 48616.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cirratus (bacteria) / Strain: MD227-A9 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: A0A0A6YVN3*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1299 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.1M Tris-HCl, pH 8.3, 1.175M Lithium Sulfate, 10mM L-Met, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97939 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 14, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 154262 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 20.86 Å2 / Rmerge(I) obs: 0.116 / Χ2: 1.011 / Net I/σ(I): 9.94
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-2.070.7940.6192.3118375251370470970.71791.7
2.07-2.220.8910.4173.4418637348298468150.48296.9
2.22-2.390.9380.2974.7217311844694434910.34397.3
2.39-2.620.9640.2176.3416071641394403960.25197.6
2.62-2.930.9830.1468.9614511137310365260.16997.9
2.93-3.380.9930.08814.4312818033016324160.10298.2
3.38-4.130.9960.05422.2110756027844274130.06398.5
4.13-5.820.9970.04426.658306621558212430.05198.5
5.82-500.9980.03829.964548712022117580.04597.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVEphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.955→45.177 Å / SU ML: 0.22 / σ(F): 1.92 / Phase error: 24.11 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 7713 5 %random
Rwork0.1943 ---
obs0.1961 154238 97.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 269.01 Å2 / Biso mean: 22.2453 Å2 / Biso min: 5.71 Å2
Refinement stepCycle: LAST / Resolution: 1.955→45.177 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13068 0 87 1299 14454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00813433
X-RAY DIFFRACTIONf_angle_d1.0618273
X-RAY DIFFRACTIONf_chiral_restr0.0421997
X-RAY DIFFRACTIONf_plane_restr0.0052406
X-RAY DIFFRACTIONf_dihedral_angle_d13.5964804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.955-1.97720.32822010.27493811401275
1.9772-2.00050.29412550.25144834508997
2.0005-2.02490.31972560.23574865512197
2.0249-2.05050.28322560.22914876513297
2.0505-2.07750.25982550.23024841509697
2.0775-2.10590.28642590.22824916517597
2.1059-2.1360.25152560.22034858511497
2.136-2.16790.27812560.21674879513597
2.1679-2.20180.27482570.2124868512597
2.2018-2.23790.27452590.2074921518097
2.2379-2.27650.21772580.19284901515997
2.2765-2.31780.24152560.1964872512898
2.3178-2.36240.24642600.19834943520398
2.3624-2.41060.24622590.20064921518098
2.4106-2.46310.2472580.20094890514898
2.4631-2.52030.24982580.20234916517498
2.5203-2.58340.24042600.20734927518798
2.5834-2.65320.25692580.20634911516998
2.6532-2.73130.26442610.21124962522398
2.7313-2.81940.22472580.21574885514398
2.8194-2.92020.26542610.20954966522798
2.9202-3.03710.27142610.21014951521299
3.0371-3.17530.24412600.20684956521699
3.1753-3.34260.24482620.19554962522499
3.3426-3.5520.21462610.18024962522399
3.552-3.82610.19822610.16354972523399
3.8261-4.21090.16712630.16074987525099
4.2109-4.81960.17692630.15624989525299
4.8196-6.06980.20782620.17684987524999
6.0698-45.1890.19082630.18064996525999

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