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- PDB-3wvr: Structure of ATP grasp protein with AMP -

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Basic information

Entry
Database: PDB / ID: 3wvr
TitleStructure of ATP grasp protein with AMP
ComponentsPGM1
KeywordsBIOSYNTHETIC PROTEIN / ATP grasp domain / LIGASE
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
Pre ATP-grasp domain / PGM1 C-terminal domain / PGM1 C-terminal domain / Pre ATP-grasp domain / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / PGM1
Similarity search - Component
Biological speciesStreptomyces cirratus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / SAD / Resolution: 2.175 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 1.2Nov 8, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)197,23125
Polymers194,4654
Non-polymers2,76721
Water8,053447
1
A: PGM1
D: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,44012
Polymers97,2322
Non-polymers1,20810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PGM1
C: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,79113
Polymers97,2322
Non-polymers1,55911
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)49,2525
Polymers48,6161
Non-polymers6354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5408
Polymers48,6161
Non-polymers9247
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: PGM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5368
Polymers48,6161
Non-polymers9207
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.600, 86.720, 94.140
Angle α, β, γ (deg.)73.870, 86.060, 68.230
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.: 17 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 0.1M Tris-HCl pH 8.1, 1.25M Lithium Sulfate, 10mM AMPPNP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionHighest resolution: 2.17 Å / Num. obs: 112313 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 29.03 Å2 / Rmerge(I) obs: 0.133 / Χ2: 1.049 / Net I/σ(I): 8.04
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.17-2.30.7910.7532.086641418653173180.87492.8
2.3-2.460.890.5352.866725817455170400.61997.6
2.46-2.660.9270.4073.696279116274159480.47198
2.66-2.910.9640.2685.255792615006147350.3198.2
2.91-3.260.9850.1538.325210513562133640.17798.5
3.26-3.760.9930.09113.054555011990118270.10698.6
3.76-4.590.9950.06617.36376451010199750.07698.8
4.59-6.460.9950.06118.6429129785077720.07199
6.460.9970.0522.6216326439343340.05898.7

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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: molecular replacement-SAD
Starting model: 3WVQ

3wvq


Resolution: 2.175→45.184 Å / SU ML: 0.29 / σ(F): 1.91 / Phase error: 28.02 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5580 5 %RANDOM
Rwork0.2017 ---
obs0.2039 111585 97.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 234.59 Å2 / Biso mean: 39.5202 Å2 / Biso min: 14.63 Å2
Refinement stepCycle: LAST / Resolution: 2.175→45.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12974 0 160 447 13581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00913417
X-RAY DIFFRACTIONf_angle_d1.15618278
X-RAY DIFFRACTIONf_chiral_restr0.051999
X-RAY DIFFRACTIONf_plane_restr0.0052396
X-RAY DIFFRACTIONf_dihedral_angle_d14.0954793
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 (%)
2.1745-2.19930.38761520.32922874302679
2.1993-2.22510.34661880.29253579376797
2.2251-2.25230.35081850.28513497368297
2.2523-2.28080.30231880.27253586377497
2.2808-2.31080.3561860.27353537372398
2.3108-2.34240.28941880.26993572376097
2.3424-2.37590.33041860.25723519370598
2.3759-2.41140.30221890.25553596378598
2.4114-2.4490.31781850.24833505369098
2.449-2.48920.28791890.23913594378398
2.4892-2.53210.31271870.25423546373398
2.5321-2.57810.32461880.2433585377398
2.5781-2.62770.36561890.2493579376898
2.6277-2.68140.27831890.23523590377998
2.6814-2.73970.28721860.2313543372998
2.7397-2.80340.28061900.22233591378198
2.8034-2.87350.27571890.21583606379598
2.8735-2.95110.24091870.21283552373998
2.9511-3.0380.26211870.22423542372998
3.038-3.1360.29451890.21683599378898
3.136-3.24810.26341870.2123544373198
3.2481-3.37810.20991880.19523575376398
3.3781-3.53180.24591880.18853567375598
3.5318-3.71790.23081870.17883551373898
3.7179-3.95070.2091840.16673506369097
3.9507-4.25550.18991860.15533537372397
4.2555-4.68340.17331860.14393517370397
4.6834-5.36010.20511870.14923556374398
5.3601-6.74960.20641860.18653547373397
6.7496-45.19330.16731840.16423513369796
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)
12.72930.43320.38850.89840.21680.75720.0051-0.0494-0.00930.03510.04550.1477-0.0001-0.266100.26480.00940.00130.4409-0.06580.381639.249723.908616.8855
21.452-0.08450.50862.71020.45052.36260.0035-0.1453-0.15880.42020.06330.00260.21950.051200.35810.00620.00160.32290.0030.299167.37222.946436.631
32.38070.27060.41841.05310.38981.304-0.0673-0.440.65630.1719-0.10210.2728-0.3422-0.2686-0.02230.44670.03510.03090.3497-0.04120.419649.377841.682123.9352
41.9638-1.152-0.11071.52250.53731.26090.11640.2471-0.2019-0.0657-0.0256-0.04550.072-0.2321-00.1639-0.0335-0.00930.339-0.06280.29128.892324.426-18.8357
51.5159-0.0301-0.75670.85680.56251.8335-0.01170.16070.0391-0.23920.00590.1051-0.1938-0.0323-00.2144-0.0107-0.02160.184-0.03480.179657.72427.4905-32.7091
62.7947-0.7532-0.57031.16150.97491.6562-0.01430.4922-0.5909-0.1653-0.1320.2960.2431-0.2859-0.02240.3444-0.0232-0.05530.2797-0.08270.388642.70627.9208-25.17
71.972-0.1619-0.23210.70370.35770.55370.0430.3742-0.0723-0.05170.0194-0.14430.00260.128800.17420.0251-0.00070.2219-0.02630.218476.9140.2392-18.5341
80.4691-0.63290.1631.51540.29421.28780.06560.1244-0.0309-0.15120.01060.1416-0.2393-0.1637-00.29120.0584-0.00510.2816-0.03280.278346.691653.2214-18.4036
91.769-0.10180.57720.4750.07251.57360.01670.0990.20210.067-0.0381-0.0445-0.1616-0.065200.2134-0.01690.00340.1705-0.02170.208363.358144.8395-2.9268
102.6995-0.0346-0.29591.96620.83011.11550.01640.09990.5464-0.14980.0237-0.1367-0.2366-0.11700.2497-0.0139-0.03720.2369-0.07410.382180.694958.6006-1.9286
110.304-0.0448-0.19130.1144-0.0960.2464-0.42660.28990.52740.0450.13480.19-0.8231-0.47340.00170.3750.0102-0.13240.2075-0.14040.621579.828368.5607-0.274
122.34680.1170.24470.70270.1430.49560.072-0.2901-0.00410.0829-0.0305-0.13960.0350.091-00.1731-0.0149-0.00270.2187-0.05050.25483.53859.47217.0251
130.64010.4515-0.5791.7910.09431.11460.0913-0.1229-0.14250.2099-0.03680.12810.2997-0.004200.2774-0.0487-0.010.2937-0.08580.419453.4386-3.495416.7496
142.2392-1.3817-0.71371.65270.55710.70160.01350.1887-0.3849-0.0609-0.10440.1120.1288-0.0836-00.23650.0147-0.00420.2504-0.03760.268577.2692-0.4664-0.5292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 1:151 )
2X-RAY DIFFRACTION2chain A and (resid 152:249 )
3X-RAY DIFFRACTION3chain A and (resid 250:430 )
4X-RAY DIFFRACTION4chain B and (resid 1:118 )
5X-RAY DIFFRACTION5chain B and (resid 119:249 )
6X-RAY DIFFRACTION6chain B and (resid 250:428 )
7X-RAY DIFFRACTION7chain C and (resid 1:164 )
8X-RAY DIFFRACTION8chain C and (resid 165:249 )
9X-RAY DIFFRACTION9chain C and (resid 250:344 )
10X-RAY DIFFRACTION10chain C and (resid 345:424 )
11X-RAY DIFFRACTION11chain C and (resid 425:433 )
12X-RAY DIFFRACTION12chain D and (resid 1:164 )
13X-RAY DIFFRACTION13chain D and (resid 165:249 )
14X-RAY DIFFRACTION14chain D and (resid 250:430 )

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