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- PDB-3rzi: The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synt... -

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Basic information

Entry
Database: PDB / ID: 3rzi
TitleThe structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis cocrystallized and complexed with phenylalanine and tryptophan
ComponentsProbable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
KeywordsTRANSFERASE / DAH7P SYNTHASE / SHIKIMATE PATHWAY / AROMATIC BIOSYNTHESIS / EVOLUTIONARY RELATIONSHIPS / PHE+TRP-BOUND / AUGMENTED TIM-BARREL STRUCTURE / STRUCTURAL GENOMICS / MYCOBACTERIUM TUBERCULOSIS STRUCTURAL PROTEOMICS PROJECT / XMTB / TIM Barrel
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / protein homooligomerization / manganese ion binding / plasma membrane / cytosol
Similarity search - Function
DAHP synthetase, class II / Class-II DAHP synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / PHENYLALANINE / PHOSPHATE ION / TRYPTOPHAN / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsJiao, W. / Jameson, G.B. / Hutton, R.D. / Parker, E.J.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Dynamic cross-talk among remote binding sites: the molecular basis for unusual synergistic allostery.
Authors: Jiao, W. / Hutton, R.D. / Cross, P.J. / Jameson, G.B. / Parker, E.J.
History
DepositionMay 11, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 1, 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_asym_id / _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_asym_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_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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
B: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,63124
Polymers101,4012
Non-polymers2,23122
Water8,917495
1
A: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
B: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
hetero molecules

A: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
B: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,26248
Polymers202,8014
Non-polymers4,46144
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area12160 Å2
ΔGint-86 kcal/mol
Surface area63410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)207.560, 207.560, 66.977
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

21B-595-

HOH

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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 6 / Auth seq-ID: 20 - 462 / Label seq-ID: 20 - 462

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG / DAHP synthetase / phenylalanine-repressible


Mass: 50700.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: aroG, Rv2178c / Plasmid: PPROEXHTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 8 types, 517 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 495 / 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: 4.11 Å3/Da / Density % sol: 70.05 % / Mosaicity: 0.427 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20MM BTP, 150MM NACL, 0.5MM TCEP, 0.2MM PEP, 0.1MM MNCL2, 0.1M HEPES, 0.8M NAK PHOSPHATE, pH 8.0, 0.1MM Trp and Phe ligands, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 15, 2010 / Details: AXCo PX70 capillary optic
RadiationMonochromator: AxCo PX70 capillary optic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→31.88 Å / Num. obs: 119335 / % possible obs: 99.2 % / Redundancy: 3.96 % / Rmerge(I) obs: 0.084 / Χ2: 0.96 / Net I/σ(I): 8.7 / Scaling rejects: 12124
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2Rejects% possible all
1.95-2.022.980.4422.334703114401.1959995.5
2.02-2.13.880.4162.746903117911.16121098.9
2.1-2.193.930.376347914118531.14135299.4
2.19-2.313.970.333.549103119871.13149799.5
2.31-2.464.050.2624.349616119391.04123499.8
2.46-2.644.090.2035.450393119940.99131299.9
2.64-2.914.140.1367.751103120390.93127599.9
2.91-3.334.180.08611.551601120310.821310100
3.33-4.24.220.05117.952168121100.72107299.9
4.2-31.884.130.03825.251436121510.66126398.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.19 Å31.68 Å
Translation2.19 Å31.68 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.4SSIdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B7O, 3KGF

2b7o

3kgf


Resolution: 1.95→31.88 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.164 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.018 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.168 6034 5 %RANDOM
Rwork0.1529 ---
all0.1536 ---
obs0.1536 113806 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 102.78 Å2 / Biso mean: 33.9347 Å2 / Biso min: 5.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.95→31.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7011 0 136 495 7642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0217449
X-RAY DIFFRACTIONr_bond_other_d0.0010.025001
X-RAY DIFFRACTIONr_angle_refined_deg1.9621.96110143
X-RAY DIFFRACTIONr_angle_other_deg2.027312140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.865939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.85123.352352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.921151182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1671572
X-RAY DIFFRACTIONr_chiral_restr0.1310.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.0218419
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021508
X-RAY DIFFRACTIONr_mcbond_it1.9981.54668
X-RAY DIFFRACTIONr_mcbond_other0.5061.51869
X-RAY DIFFRACTIONr_mcangle_it2.85527521
X-RAY DIFFRACTIONr_scbond_it4.51232781
X-RAY DIFFRACTIONr_scangle_it6.0534.52622
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5573 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.325
LOOSE THERMAL3.1110
LS refinement shellResolution: 1.948→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1 439 -
Rwork0.093 8077 -
all-8516 -
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)
10.0629-0.108-0.01030.1982-0.02660.1678-0.0167-0.0132-0.01120.01920.02370.01660.0260.0142-0.0070.0211-0.00580.00410.0403-0.00710.033-80.853876.28859.7886
20.98890.0227-0.03030.35420.05610.2095-0.00090.00670.04130.00670.0010.0315-0.0254-0.0365-0.00010.0151-0.0016-0.0130.02950.00180.0242-83.539871.5979-22.2388
32.0268-0.5414-0.46440.16310.12150.1076-0.0515-0.02640.05250.04120.0445-0.00440.01070.00510.0070.03910.01160.00940.05920.00340.0366-99.692982.94295.3327
40.1640.0482-0.05460.1118-0.08090.0640.0035-0.0070.03560.0040.0170.01680.0003-0.0035-0.02050.0172-0.00210.00790.0355-0.00780.0591-80.503296.35761.8522
50.32310.58370.07411.3742-0.25150.4969-0.0003-0.0532-0.0582-0.1067-0.0381-0.12070.0707-0.04040.03840.0263-0.0207-0.00040.03970.01310.0698-85.166952.1752-12.8324
60.16550.06880.03270.03330.02350.03620.00490.0074-0.02920.00290.006-0.0145-0.0078-0.0026-0.01090.0252-0.00460.00080.0296-0.00020.0647-64.384362.3421-17.1323
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 80
2X-RAY DIFFRACTION2B1 - 80
3X-RAY DIFFRACTION3A127 - 167
4X-RAY DIFFRACTION4A81 - 126
5X-RAY DIFFRACTION4A168 - 462
6X-RAY DIFFRACTION5B127 - 167
7X-RAY DIFFRACTION6B81 - 126
8X-RAY DIFFRACTION6B168 - 462

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