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- PDB-4adu: Crystal structure of plasmodial PLP synthase with bound R5P inter... -

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Basic information

Entry
Database: PDB / ID: 4adu
TitleCrystal structure of plasmodial PLP synthase with bound R5P intermediate
ComponentsPYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
KeywordsTRANSFERASE / SYNTHASE / PYRIDOXAL 5-PHOSPHATE BIOSYNTHESIS
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / RIBOSE-5-PHOSPHATE / :
Function and homology information
Biological speciesPLASMODIUM BERGHEI (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsGuedez, G. / Sinning, I. / Tews, I.
CitationJournal: Structure / Year: 2012
Title: Assembly of the Eukaryotic Plp-Synthase Complex from Plasmodium and Activation of the Pdx1 Enzyme.
Authors: Guedez, G. / Hipp, K. / Windeisen, V. / Derrer, B. / Gengenbacher, M. / Boettcher, B. / Sinning, I. / Kappes, B. / Tews, I.
History
DepositionJan 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 1.2May 15, 2024Group: Advisory / Category: database_PDB_caveat
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
B: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2379
Polymers65,4662
Non-polymers7717
Water2,756153
1
A: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
B: PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)397,41954
Polymers392,79612
Non-polymers4,62342
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation6_555-x,-x+y,-z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_555x-y,-y,-z1
Buried area57290 Å2
ΔGint-81.6 kcal/mol
Surface area111470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.471, 180.471, 102.042
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein PYRIDOXINE BIOSYNTHETIC ENZYME PDX1 HOMOLOGUE, PUTATIVE


Mass: 32733.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PLASMODIUM BERGHEI (eukaryote) / Strain: NK65 / Plasmid: PET21-A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q4Z0E8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar ChemComp-R5P / RIBOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRIBOSE 5-PHOSPHATE (R5P): LYS 84 FORMING SCHIFF BASE LINKAGE WITH R5P

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.1 M BICINE PH 8.5, 1.6 M LICL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.88
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 22508 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.6
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 97.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NV1

2nv1


Resolution: 2.44→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 18.164 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.459 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1212 5.1 %RANDOM
Rwork0.19335 ---
obs0.19629 22508 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.485 Å2
Baniso -1Baniso -2Baniso -3
1--1.54 Å2-0.77 Å20 Å2
2---1.54 Å20 Å2
3---2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.44→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4213 0 46 153 4412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224306
X-RAY DIFFRACTIONr_bond_other_d0.0020.022964
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9885784
X-RAY DIFFRACTIONr_angle_other_deg1.11837305
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9225.238168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.77215824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9591522
X-RAY DIFFRACTIONr_chiral_restr0.080.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024674
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
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_it0.6681.52730
X-RAY DIFFRACTIONr_mcbond_other0.0951.51130
X-RAY DIFFRACTIONr_mcangle_it1.2824395
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.93631576
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.3084.51389
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: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 90 -
Rwork0.264 1612 -
obs--98.5 %
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)
10.7456-0.3440.15780.84830.07260.37520.0528-0.03170.10260.128-0.0399-0.11440.0306-0.0187-0.01280.0545-0.014-0.01460.03-0.0180.040425.575828.741422.251
20.3613-0.05290.04960.9986-0.32920.34690.00330.0774-0.0105-0.11960.0247-0.1945-0.00480.0213-0.0280.0697-0.00430.07410.0236-0.01460.097836.86377.9103-22.48
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 301
2X-RAY DIFFRACTION2B15 - 301

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