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- PDB-3pfp: Structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase... -

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Basic information

Entry
Database: PDB / ID: 3pfp
TitleStructure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis in complex with an active site inhibitor
ComponentsProbable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / Shikimate pathway / Mycobacterium tuberculosis / DAH7P synthase / Aromatic biosynthesis / TIM barrel / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
(2S)-2,7-bis(phosphonooxy)heptanoic acid / (2R)-2,7-bis(phosphonooxy)heptanoic acid / : / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsReichau, S. / Jiao, W. / Walker, S.R. / Hutton, R.D. / Parker, E.J. / Baker, E.N.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Potent inhibitors of a shikimate pathway enzyme from Mycobacterium tuberculosis: combining mechanism- and modeling-based design
Authors: Reichau, S. / Jiao, W. / Walker, S.R. / Hutton, R.D. / Baker, E.N. / Parker, E.J.
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Database references / Structure summary
Revision 1.3Nov 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 / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_ref_seq_dif.details / _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)103,18710
Polymers101,6572
Non-polymers1,5308
Water9,980554
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)206,37420
Polymers203,3144
Non-polymers3,06016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11600 Å2
ΔGint-90 kcal/mol
Surface area65550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.579, 203.579, 66.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-499-

HOH

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

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROHISHISAA19 - 19521 - 197
21PROPROHISHISBB19 - 19521 - 197
12PROPROVALVALAA209 - 233211 - 235
22PROPROVALVALBB209 - 233211 - 235
13ALAALASERSERAA241 - 262243 - 264
23ALAALASERSERBB241 - 262243 - 264
14LEULEUARGARGAA271 - 461273 - 463
24LEULEUARGARGBB271 - 461273 - 463

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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: 50828.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: aroG, Rv2178c / Plasmid: pProExHTa / Production host: Escherichia coli (E. coli)
References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 6 types, 562 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-035 / (2S)-2,7-bis(phosphonooxy)heptanoic acid


Mass: 322.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O10P2
#4: Chemical ChemComp-036 / (2R)-2,7-bis(phosphonooxy)heptanoic acid


Mass: 322.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O10P2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 554 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details035(A 463) AND 036(A 716) ARE TWO ENANTIOMERS OF THE RACEMIC MIXTURE USED FOR CRYSTALLIZATION AND ...035(A 463) AND 036(A 716) ARE TWO ENANTIOMERS OF THE RACEMIC MIXTURE USED FOR CRYSTALLIZATION AND MODELED AT HALF OCCUPANCY INTO THE SAME ACTIVE SITE. 036(B 463) AND 035(B 771) ARE TWO ENANTIOMERS OF THE RACEMIC MIXTURE USED FOR CRYSTALLIZATION AND MODELED AT HALF OCCUPANCY INTO THE SAME ACTIVE SITE.

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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: 3.91 Å3/Da / Density % sol: 68.56 % / Mosaicity: 0.12 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.5M ammonium sulfate, 0.4M inhibitor, 12%(v/v) glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.35→51.134 Å / Num. all: 65888 / Num. obs: 65888 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 26.5 Å2 / Rsym value: 0.13 / Net I/σ(I): 15.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.35-2.4811.20.410.3921.910701995690.1220.410.3926.7100
2.48-2.6311.20.3170.3022.410074190170.0940.3170.3028.3100
2.63-2.8111.20.2380.2273.29493485060.0710.2380.22710.6100
2.81-3.0311.10.1740.1664.48838879510.0520.1740.16613.3100
3.03-3.3211.10.1260.12168095073200.0380.1260.12116.7100
3.32-3.72110.1050.16.77264966060.0320.1050.120.9100
3.72-4.2910.90.10.0966.66364458520.030.10.09624.2100
4.29-5.2510.40.090.0867.25184149810.0280.090.08624.9100
5.25-7.4310.80.0780.0748.34196838900.0240.0780.07424.7100
7.43-53.08310.90.0660.0638.82403621960.020.0660.06329.599.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2B7O

2b7o


Resolution: 2.35→50.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.927 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8983 / SU B: 9.029 / SU ML: 0.102 / SU R Cruickshank DPI: 0.1909 / SU Rfree: 0.1639 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.19576 3273 5 %RANDOM
Rwork0.16246 ---
obs0.16412 62565 99.96 %-
all-65888 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 123.48 Å2 / Biso mean: 25.972 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.35→50.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7067 0 84 554 7705
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217369
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2141.96810045
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6345940
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08823.493335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.163151158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4231566
X-RAY DIFFRACTIONr_chiral_restr0.0850.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215678
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.931.54661
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75927492
X-RAY DIFFRACTIONr_scbond_it2.33332708
X-RAY DIFFRACTIONr_scangle_it4.0174.52552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

NumberTypeRms dev position (Å)Weight position
1647medium positional0.180.5
1486loose positional0.425
1647medium thermal1.222
1486loose thermal1.2310
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 229 -
Rwork0.184 4614 -
all-4843 -
obs--100 %
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)
10.6544-0.52761.70511.2711-2.23515.39480.0288-0.1543-0.01880.0950.19210.1781-0.1154-0.4483-0.2210.12160.04730.01370.1048-0.00660.053113.1727106.189215.4373
20.47430.0181-0.14890.30960.11160.38370.0165-0.01420.00520.01560.0068-0.0356-0.01320.0026-0.02330.0960.0205-0.00130.0723-0.01410.054834.0027110.273514.7355
30.40860.01960.05170.88180.1290.13410.05650.02710.0017-0.0846-0.0103-0.008-0.0320.0099-0.04620.12320.01860.0120.0754-0.01230.042729.8445117.90937.3313
41.2012-2.4203-1.258111.1163.18091.38990.1338-0.0130.0601-0.008-0.12250.2187-0.0840.0186-0.01130.11130.06390.06550.12040.00120.11857.9636111.4212-3.2529
51.25320.4514-0.33650.86660.58861.5256-0.0256-0.0507-0.12790.101-0.0026-0.06470.09690.04820.02830.09740.0229-0.0090.07730.00130.044432.5176107.262122.5294
60.6125-0.12830.02590.4806-0.13860.81430.0445-0.08670.13350.00290.0373-0.1265-0.05390.0428-0.08180.0858-0.0109-0.01210.067-0.04610.108346.2536122.100118.0399
75.19732.36057.48611.07373.398510.7866-0.2563-0.44510.005-0.20320.04680.0127-0.7381-0.66350.20960.39730.28110.27560.23590.15820.241510.4885116.95988.361
83.33111.6443-0.9931.6909-1.14270.97990.0336-0.17130.2770.0623-0.07670.1083-0.14890.02530.04310.10650.0629-0.03030.0773-0.00090.087116.1717110.6305-17.4923
90.3957-0.1904-0.02470.39070.15070.18710.0191-0.0187-0.02970.0145-0.00730.0172-0.0165-0.0199-0.01180.07280.0177-0.00030.08970.00440.058318.317395.1649-1.6836
108.10610.94060.25080.481-0.06480.03330.024-0.4930.3050.0101-0.03230.0580.0045-0.00750.00840.07860.03790.01160.13540.01780.069534.165772.91456.8033
110.1692-0.29480.04670.81290.08150.6150.03680.0447-0.0524-0.0413-0.0329-0.0014-0.03130.0181-0.00380.0460.0288-0.01530.0857-0.0210.060118.773887.934-15.6308
122.319-0.3627-0.41870.32660.09360.4903-0.0131-0.1237-0.10870.06610.05090.03880.0496-0.0007-0.03780.0647-0.0033-0.00780.06890.00810.104614.802176.84592.5098
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 24
2X-RAY DIFFRACTION2A25 - 135
3X-RAY DIFFRACTION3A136 - 207
4X-RAY DIFFRACTION4A208 - 237
5X-RAY DIFFRACTION5A238 - 307
6X-RAY DIFFRACTION6A308 - 462
7X-RAY DIFFRACTION7B-1 - 11
8X-RAY DIFFRACTION8B12 - 39
9X-RAY DIFFRACTION9B40 - 194
10X-RAY DIFFRACTION10B195 - 237
11X-RAY DIFFRACTION11B238 - 408
12X-RAY DIFFRACTION12B409 - 462

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