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- PDB-2r85: Crystal structure of PurP from Pyrococcus furiosus complexed with AMP -

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Basic information

Entry
Database: PDB / ID: 2r85
TitleCrystal structure of PurP from Pyrococcus furiosus complexed with AMP
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 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain ...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 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / 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 / 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: 1.7 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
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_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.pdbx_ptnr1_label_alt_id / _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_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)78,67514
Polymers76,6962
Non-polymers1,97812
Water11,746652
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)118,01221
Polymers115,0443
Non-polymers2,96818
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 area19480 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)118,01221
Polymers115,0443
Non-polymers2,96818
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 area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.205, 123.205, 376.298
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-649-

HOH

21A-678-

HOH

31A-692-

HOH

41B-642-

HOH

51B-668-

HOH

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 , 5 types, 664 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.: 4 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#5: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 3.58 Å3/Da / Density % sol: 65.67 %
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: 1.7→50 Å / Num. all: 119607 / Num. obs: 119574 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.052 / Χ2: 0.957 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.7660.284116210.466197
1.76-1.837.10.22117810.482198.6
1.83-1.917.20.153118310.529198.7
1.91-2.027.20.111118810.592198.9
2.02-2.147.20.079118760.667199.1
2.14-2.317.20.062119610.765199.3
2.31-2.547.10.052120100.882199.5
2.54-2.917.10.046120701.124199.7
2.91-3.6670.044121691.954199.8
3.66-506.70.034124072.05199.1

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2R7K

2r7k


Resolution: 1.7→37.88 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.446 / SU ML: 0.043 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.079 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.186 6079 5.1 %RANDOM
Rwork0.165 ---
all0.167 119607 --
obs0.167 119574 98.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.7→37.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5356 0 128 652 6136
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226086
X-RAY DIFFRACTIONr_angle_refined_deg1.1428302
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4915746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12123.746283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.906151093
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1131548
X-RAY DIFFRACTIONr_chiral_restr0.0780.2887
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024666
X-RAY DIFFRACTIONr_nbd_refined0.2010.22764
X-RAY DIFFRACTIONr_nbtor_refined0.3050.24240
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1050.2615
X-RAY DIFFRACTIONr_metal_ion_refined0.0960.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1640.2170
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0890.256
X-RAY DIFFRACTIONr_mcbond_it0.4921.53588
X-RAY DIFFRACTIONr_mcangle_it0.95425886
X-RAY DIFFRACTIONr_scbond_it1.52932596
X-RAY DIFFRACTIONr_scangle_it2.5964.52416
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 437 -
Rwork0.224 8059 -
all-8496 -
obs--96.47 %
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)
10.1060.005-0.01940.0671-0.03210.19970.00380.01530.0096-0.00780.00380.02930.0012-0.0406-0.0077-0.01980.0044-0.00430.00180.006-0.006642.730240.141518.0979
20.2249-0.02640.08170.1393-0.07080.325-0.0059-0.04380.00260.03010.00460.0233-0.0261-0.08210.0012-0.01790.00340.01220.0184-0.0049-0.025242.649939.950977.4023
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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