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- PDB-3zzm: Crystal structure of Mycobacterium tuberculosis PurH with a novel... -

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Basic information

Entry
Database: PDB / ID: 3zzm
TitleCrystal structure of Mycobacterium tuberculosis PurH with a novel bound nucleotide CFAIR, at 2.2 A resolution.
ComponentsBIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH
KeywordsTRANSFERASE / HYDROLASE / PURINE BIOSYNTHESIS / TUBERCULOSIS
Function / homology
Function and homology information


phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process / plasma membrane / cytosol
Similarity search - Function
AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. ...AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Cytidine Deaminase; domain 2 / Cytidine deaminase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-JLN / : / PHOSPHATE ION / Bifunctional purine biosynthesis protein PurH / Bifunctional purine biosynthesis protein PurH
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLe Nours, J. / Bulloch, E.M.M. / Zhang, Z. / Greenwood, D.R. / Middleditch, M.J. / Dickson, J.M.J. / Baker, E.N.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural Analyses of a Purine Biosynthetic Enzyme from Mycobacterium Tuberculosis Reveal a Novel Bound Nucleotide.
Authors: Le Nours, J. / Bulloch, E.M.M. / Zhang, Z. / Greenwood, D.R. / Middleditch, M.J. / Dickson, J.M.J. / Baker, E.N.
History
DepositionSep 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references / Other
Revision 1.2Dec 14, 2011Group: Database references
Revision 1.3Nov 27, 2013Group: Source and taxonomy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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_conn.ptnr2_label_seq_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: BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH
B: BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,8027
Polymers110,1702
Non-polymers6325
Water7,278404
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12280 Å2
ΔGint-63.9 kcal/mol
Surface area39080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.594, 108.220, 130.634
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9711, -0.2038, 0.1243), (-0.2043, 0.44, -0.8744), (0.1235, -0.8745, -0.469)
Vector: 141.8, 74.83, 90.26)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH / PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE / AICAR TRANSFORMYLASE / IMP ...PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE / AICAR TRANSFORMYLASE / IMP CYCLOHYDROLASE / ATIC / IMP SYNTHASE / INOSINICASE


Mass: 55084.949 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P67541, UniProt: P9WHM7*PLUS, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase

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Non-polymers , 5 types, 409 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-JLN / 5-(FORMYLAMINO)-1-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-1H-IMIDAZOLE-4-CARBOXYLIC ACID


Type: RNA linking / Mass: 367.206 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N3O10P
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.3 Å3/Da / Density % sol: 46.57 % / Description: NONE
Crystal growpH: 6.5
Details: 24-34% PEG 8000 0.2M SODIUM ACETATE 0.1M SODIUM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 54907 / % possible obs: 98.1 % / Observed criterion σ(I): 2 / Redundancy: 9.8 % / Biso Wilson estimate: 40.88 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 30.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 87

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Processing

Software
NameVersionClassification
BUSTER2.8.0refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1PKX AND 1ZCZ

1pkx

1zcz


Resolution: 2.2→28.76 Å / Cor.coef. Fo:Fc: 0.9438 / Cor.coef. Fo:Fc free: 0.926 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=K GOL JLN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=8147. NUMBER WITH APPROX DEFAULT CCP4 ATOM ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=K GOL JLN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=8147. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=30. NUMBER TREATED BY BAD NON- BONDED CONTACTS=2. RESIDUES A1 TO A3 AND B1 TO B5 WERE NOT MODELLED FOR LACK OF CLEAR ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.2355 2779 5.07 %RANDOM
Rwork0.1976 ---
obs0.1995 54774 --
Displacement parametersBiso mean: 42.57 Å2
Baniso -1Baniso -2Baniso -3
1-2.6616 Å20 Å20 Å2
2---7.2281 Å20 Å2
3---4.5665 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: LAST / Resolution: 2.2→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7700 0 37 404 8141
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017945HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0310853HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3552SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes180HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1211HARMONIC5
X-RAY DIFFRACTIONt_it7945HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.32
X-RAY DIFFRACTIONt_other_torsion2.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1058SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9737SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3055 186 5.27 %
Rwork0.2441 3342 -
all0.2472 3528 -
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)
10.3963-0.23570.25560.726-0.30760.7084-0.00950.00950.085-0.0154-0.0397-0.1106-0.03920.11520.0492-0.15130.0251-0.00060.0098-0.016-0.086573.099195.246711.3289
20.39930.1131-0.01320.6523-0.21670.6590.01490.091-0.03380.00610.01650.0849-0.1054-0.051-0.0314-0.1560.022-0.0023-0.0031-0.0474-0.099152.810691.930610.5439
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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