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- PDB-4ucg: NmeDAH7PS R126S variant -

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Basic information

Entry
Database: PDB / ID: 4ucg
TitleNmeDAH7PS R126S variant
ComponentsPHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
KeywordsTRANSFERASE / SHIKIMATE PATHWAY / DAHPS / DAH7PS
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / PHOSPHOENOLPYRUVATE / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCross, P.J. / Heyes, L.C. / Zhang, S. / Nazmi, A.R. / Parker, E.J.
CitationJournal: Plos One / Year: 2016
Title: The Functional Unit of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase is Dimeric.
Authors: Cross, P.J. / Heyes, L.C. / Zhang, S. / Nazmi, A.R.
History
DepositionDec 3, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Dec 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_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
C: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
D: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,17319
Polymers154,5684
Non-polymers1,60515
Water13,241735
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-110.3 kcal/mol
Surface area44000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.949, 132.660, 147.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A16 - 350
2116B16 - 350
1126A16 - 350
2126C16 - 350
1136A16 - 350
2136D16 - 350

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.052162, -0.998636, -0.002101), (-0.998595, 0.05214, 0.009493), (-0.00937, 0.002593, -0.999953)20.63235, 19.83943, -34.71185

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE / 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / DAHP SYNTHASE / PHOSPHO-2-KETO-3- ...3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / DAHP SYNTHASE / PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE / DAH7PS


Mass: 38642.020 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 5 types, 750 molecules

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


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 735 / 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: 2.54 Å3/Da / Density % sol: 51.69 % / Description: NONE
Crystal growpH: 7.3
Details: 0.1 M TRIS HCL (PH 7.3), 0.2 M TRIMETHYL-AMINO-N-OXIDE (TMAO), 600UM MNSO4 AND 15-20% (W/V) PEG 2000MME

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953 Å / Relative weight: 1
ReflectionResolution: 2→48.03 Å / Num. obs: 105375 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 14.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 15.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HSN

4hsn


Resolution: 2→98.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.44 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5260 5 %RANDOM
Rwork0.18007 ---
obs0.18206 100004 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.949 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.38 Å2
Refinement stepCycle: LAST / Resolution: 2→98.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10136 0 81 735 10952
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910498
X-RAY DIFFRACTIONr_bond_other_d0.0010.029943
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.96414243
X-RAY DIFFRACTIONr_angle_other_deg0.775322841
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.27651355
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.9723.991456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.018151732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6711568
X-RAY DIFFRACTIONr_chiral_restr0.0750.21600
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112038
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022354
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_it1.362.5295393
X-RAY DIFFRACTIONr_mcbond_other1.362.5295392
X-RAY DIFFRACTIONr_mcangle_it2.1123.7846748
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.8522.7445105
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
14935loose positional0.255
24890loose positional0.315
34966loose positional0.345
14935loose thermal2.0210
24890loose thermal4.6710
34966loose thermal3.8110
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 377 -
Rwork0.284 7301 -
obs--99.99 %
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)
10.3019-0.01360.16630.23460.1230.60370.00650.01220.03120.0553-0.05960.03950.0050.04080.05310.0908-0.00490.00620.0580.00350.021847.725-14.829-3.129
20.1915-0.26340.09570.55070.20140.7870.0050.057-0.0436-0.0128-0.13780.16890.0689-0.02850.13280.07010.0135-0.02390.0468-0.05380.081832.764-28.63-31.77
30.6809-0.1408-0.15690.15160.0650.7450.03180.10660.00530.0669-0.02650.0412-0.0662-0.0314-0.00530.07980.04550.03460.08520.01290.0312-0.28813.378-0.636
40.048-0.18430.18751.6507-0.73161.3777-0.08070.02730.00660.12810.11260.1014-0.15470.1011-0.03190.1154-0.0543-0.030.08270.03420.02037.54720.727-34.617
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 350
2X-RAY DIFFRACTION2B17 - 349
3X-RAY DIFFRACTION3C16 - 349
4X-RAY DIFFRACTION4D17 - 349

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