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- PDB-2r84: Crystal structure of PurP from Pyrococcus furiosus complexed with... -

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Basic information

Entry
Database: PDB / ID: 2r84
TitleCrystal structure of PurP from Pyrococcus furiosus complexed with AMP and AICAR
ComponentsPurP protein PF1517
KeywordsUNKNOWN FUNCTION / ATP-grasp superfamily
Function / homology
Function and homology information


formate-phosphoribosylaminoimidazolecarboxamide ligase / ligase activity, forming carbon-nitrogen bonds / 'de novo' IMP biosynthetic process / magnesium ion binding / ATP binding
Similarity search - Function
IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily ...IMP biosynthesis enzyme PurP, C-terminal / IMP biosynthesis enzyme PurP, N-terminal / IMP biosynthesis enzyme PurP / Protein of unknown function (DUF1246) / Domain of unknown function (DUF1297) / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsZhang, Y. / White, R.H. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii.
Authors: Zhang, Y. / White, R.H. / Ealick, S.E.
History
DepositionSep 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_special_symmetry / struct_conn / struct_ncs_dom_lim / struct_site
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 / _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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: PurP protein PF1517
B: PurP protein PF1517
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,53913
Polymers76,6962
Non-polymers1,84211
Water11,241624
1
A: PurP protein PF1517
hetero molecules

A: PurP protein PF1517
hetero molecules

A: PurP protein PF1517
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,98521
Polymers115,0443
Non-polymers2,94118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area20210 Å2
MethodPISA
2
B: PurP protein PF1517
hetero molecules

B: PurP protein PF1517
hetero molecules

B: PurP protein PF1517
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,63118
Polymers115,0443
Non-polymers2,58615
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area18770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.671, 123.671, 375.359
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-662-

HOH

21A-694-

HOH

31A-709-

HOH

41A-879-

HOH

51B-652-

HOH

61B-704-

HOH

71B-823-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 120 - 128 / Label seq-ID: 120 - 128

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
Detailsbiological assembly is a hexamer or a trimer from the asymmetric unit by the operations: (x,y,z), (-y,x-y,z +(1 1 0)), (-x+y,-x,z)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PurP protein PF1517


Mass: 38348.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: T7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U0R7

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Non-polymers , 6 types, 635 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical ChemComp-AMZ / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / AICAR


Mass: 338.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N4O8P
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 3.6 Å3/Da / Density % sol: 65.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% MPD, 200 mM NaCl, 100 mM Tris, pH 7.0, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 85987 / Num. obs: 85981 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.074 / Χ2: 1.058 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.975.90.36581020.665194.4
1.97-2.0570.26784770.619199.4
2.05-2.147.20.20486030.85199.8
2.14-2.257.20.15685860.8081100
2.25-2.397.20.12585840.8331100
2.39-2.587.20.10386320.8641100
2.58-2.847.20.0886240.9331100
2.84-3.257.20.06287041.199199.9
3.25-4.097.10.05587202.094199.9
4.09-506.90.03789551.609199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.3.0037refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R7K

2r7k


Resolution: 1.9→37.9 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.943 / SU B: 4.012 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.113 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.195 4365 5.1 %RANDOM
Rwork0.174 ---
all0.175 85987 --
obs0.175 85981 99.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.777 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20.34 Å20 Å2
2--0.68 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5215 0 118 624 5957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225832
X-RAY DIFFRACTIONr_angle_refined_deg1.0722.0077958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345700
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.29623.741270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.298151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5731544
X-RAY DIFFRACTIONr_chiral_restr0.0730.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024448
X-RAY DIFFRACTIONr_nbd_refined0.1880.22644
X-RAY DIFFRACTIONr_nbtor_refined0.30.24014
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0910.2677
X-RAY DIFFRACTIONr_metal_ion_refined0.0750.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.2160
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.276
X-RAY DIFFRACTIONr_mcbond_it0.3421.53443
X-RAY DIFFRACTIONr_mcangle_it0.66725637
X-RAY DIFFRACTIONr_scbond_it0.95832483
X-RAY DIFFRACTIONr_scangle_it1.6714.52321
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A36MEDIUM POSITIONAL0.120.5
1B37LOOSE POSITIONAL0.525
2A36MEDIUM THERMAL0.782
2B37LOOSE THERMAL0.5710
LS refinement shellResolution: 1.9→1.953 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 303 -
Rwork0.228 5446 -
all-5749 -
obs--91.05 %
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)
10.25880.0217-0.080.1822-0.07640.42540.00640.04030.0123-0.02760.0140.0565-0.0015-0.0886-0.0204-0.0320.0058-0.012-0.00060.0127-0.007942.875940.011618.0795
20.5397-0.05820.19390.375-0.11630.7173-0.0017-0.10750.01890.08610.00240.0653-0.0287-0.1659-0.0007-0.02530.00220.02680.0236-0.0099-0.038643.165739.59975.835
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3341 - 334
2X-RAY DIFFRACTION2BB1 - 3341 - 334

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