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- PDB-2y85: CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL IS... -

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Basic information

Entry
Database: PDB / ID: 2y85
TitleCRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS PHOSPHORIBOSYL ISOMERASE WITH BOUND RCDRP
ComponentsPHOSPHORIBOSYL ISOMERASE A
KeywordsISOMERASE / BIFUNCTIONAL ENZYME / TRYPTOPHAN BIOSYNTHESIS / HISTIDINE BIOSYNTHESIS / TIM-BARREL / AROMATIC AMINO ACID BIOSYNTHESIS
Function / homology
Function and homology information


phosphoribosylanthranilate isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / phosphoribosylanthranilate isomerase activity / L-histidine biosynthetic process / L-tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA/PriA, Actinobacteria / HisA/PriA, bacterial-type / Histidine biosynthesis, HisA-like / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-137 / Phosphoribosyl isomerase A / Phosphoribosyl isomerase A
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKuper, J. / Geerlof, A. / Wilmanns, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Bisubstrate Specificity in Histidine/Tryptophan Biosynthesis Isomerase from Mycobacterium Tuberculosis by Active Site Metamorphosis.
Authors: Due, A.V. / Kuper, J. / Geerlof, A. / Kries, J.P. / Wilmanns, M.
History
DepositionFeb 3, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_sheet / 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_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORIBOSYL ISOMERASE A
B: PHOSPHORIBOSYL ISOMERASE A
C: PHOSPHORIBOSYL ISOMERASE A
D: PHOSPHORIBOSYL ISOMERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,43523
Polymers102,6354
Non-polymers1,80019
Water3,387188
1
A: PHOSPHORIBOSYL ISOMERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1146
Polymers25,6591
Non-polymers4565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOSPHORIBOSYL ISOMERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0915
Polymers25,6591
Non-polymers4334
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PHOSPHORIBOSYL ISOMERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1146
Polymers25,6591
Non-polymers4565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: PHOSPHORIBOSYL ISOMERASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1146
Polymers25,6591
Non-polymers4565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.980, 121.070, 81.140
Angle α, β, γ (deg.)90.00, 95.60, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1031, -0.4962, 0.862), (0.4512, -0.7957, -0.4041), (0.8864, 0.3474, 0.3059)-21.65, -48.9, 65.21
2given(0.1057, -0.4733, -0.8745), (-0.4459, -0.8087, 0.3838), (-0.8888, 0.3493, -0.2965)33.51, -36.66, 60.98
3given(0.9979, -0.003574, -0.06512), (0.000718, 0.999, -0.04384), (0.06521, 0.0437, 0.9969)-3.963, -22.96, 39.98

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Components

#1: Protein
PHOSPHORIBOSYL ISOMERASE A / 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE ...1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE / N-(5'-PHOSPHORIBOSYL)ANTHRANILATE ISOMERASE / PRAI / PHOSPHORIBOSYLFORMIMINO- 5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE / PRIA


Mass: 25658.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P60578, UniProt: P9WMM5*PLUS, phosphoribosylanthranilate isomerase, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-137 / 1-(O-CARBOXY-PHENYLAMINO)-1-DEOXY-D-RIBULOSE-5-PHOSPHATE


Mass: 351.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H18NO9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.23 Å3/Da / Density % sol: 44.29 % / Description: NONE
Crystal growpH: 5.7
Details: 32% PEG 6000, 0.1M SODIUM CITRATE PH 5.7, 5MM RCDRP.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 13, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 34306 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.9
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.1 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VZW

1vzw


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.866 / SU B: 24.641 / SU ML: 0.29 / Cross valid method: THROUGHOUT / ESU R: 0.719 / ESU R Free: 0.33 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28726 1731 5 %RANDOM
Rwork0.21281 ---
obs0.21663 32627 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.899 Å2
Baniso -1Baniso -2Baniso -3
1-1.15 Å20 Å20.3 Å2
2---1.21 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 107 188 7215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217105
X-RAY DIFFRACTIONr_bond_other_d0.0020.026677
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.9719663
X-RAY DIFFRACTIONr_angle_other_deg0.7733.00115251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5395929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.74423.462312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.758151084
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3451572
X-RAY DIFFRACTIONr_chiral_restr0.0660.21125
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021429
X-RAY DIFFRACTIONr_nbd_refined0.1980.21449
X-RAY DIFFRACTIONr_nbd_other0.1790.26683
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23366
X-RAY DIFFRACTIONr_nbtor_other0.0890.24197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2306
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.225
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.2103
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5311.55912
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.62327247
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.00932824
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5874.52416
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.403→2.465 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.367 112
Rwork0.275 2369
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)
11.81741.2764-0.16435.9068-0.04851.62570.01990.03230.06560.1793-0.07780.26350.153-0.09490.0579-0.1101-0.03120.0473-0.1174-0.0513-0.1063-2.722-25.86238.487
22.058-0.2327-0.53722.7048-0.59742.34140.0006-0.03480.0180.2995-0.105-0.1354-0.24770.19320.1043-0.0806-0.0494-0.0141-0.1245-0.0042-0.140611.2980.56242.409
31.36630.0517-0.13933.4984-0.8211.65890.04220.13290.0051-0.125-0.02860.10970.0874-0.0361-0.0136-0.133-0.00780.0132-0.129-0.0286-0.13061.093-2.987-1.489
41.88870.3197-0.11043.19540.82580.9345-0.1118-0.05510.0937-0.1851-0.08410.4176-0.111-0.23290.196-0.10690.0322-0.0494-0.0737-0.0467-0.0506-15.239-36.949-1.195
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 240
2X-RAY DIFFRACTION1A1247
3X-RAY DIFFRACTION2B2 - 240
4X-RAY DIFFRACTION2B1247
5X-RAY DIFFRACTION3C2 - 240
6X-RAY DIFFRACTION3C1247
7X-RAY DIFFRACTION4D2 - 240
8X-RAY DIFFRACTION4D1247

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