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- PDB-3mmt: Crystal structure of fructose bisphosphate aldolase from Bartonel... -

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Basic information

Entry
Database: PDB / ID: 3mmt
TitleCrystal structure of fructose bisphosphate aldolase from Bartonella henselae, bound to fructose bisphosphate
ComponentsFructose-bisphosphate aldolase
KeywordsHYDROLASE / SSGCID / ALDOLASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM) / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesBartonella henselae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate.
Authors: Gardberg, A. / Abendroth, J. / Bhandari, J. / Sankaran, B. / Staker, B.
History
DepositionApr 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Apr 20, 2016Group: Other
Revision 1.4Sep 6, 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_leaving_atom_flag / _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_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: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
C: Fructose-bisphosphate aldolase
D: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,5858
Polymers150,2244
Non-polymers1,3604
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9450 Å2
ΔGint-32 kcal/mol
Surface area46540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.390, 127.710, 157.630
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
12B
13C
14D

NCS domain segments:

Dom-ID: 1 / Component-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: 2FP / End label comp-ID: 2FP / Refine code: 4 / Auth seq-ID: 0 - 350 / Label seq-ID: 4

Ens-IDAuth asym-IDLabel asym-ID
1AA - E
2BB - F
3CC - G
4DD - H

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Fructose-bisphosphate aldolase


Mass: 37556.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bartonella henselae (bacteria) / Gene: BH15060, fbab, HM-1:IMSS / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8L207, fructose-bisphosphate aldolase
#2: Sugar
ChemComp-2FP / 1,6-FRUCTOSE DIPHOSPHATE (LINEAR FORM)


Type: saccharide / Mass: 340.116 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / 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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M NAOAC, 0.1 M TRIS PH 8.5, 30% PEG 4000, protein AT 21 MG/ML, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM Q315 / Detector: CCD / Date: Apr 2, 2010
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97741
20.97741
ReflectionResolution: 2.35→47.89 Å / Num. all: 61687 / Num. obs: 61670 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.9 % / Biso Wilson estimate: 35.97 Å2 / Rmerge(I) obs: 0.099
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4533 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KX6

3kx6


Resolution: 2.35→47.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.532 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.36 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3122 5.1 %RANDOM
Rwork0.177 ---
all0.179 61687 --
obs0.179 61429 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.87 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10241 0 76 498 10815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210513
X-RAY DIFFRACTIONr_bond_other_d0.0010.027019
X-RAY DIFFRACTIONr_angle_refined_deg1.181.96814262
X-RAY DIFFRACTIONr_angle_other_deg0.871317129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77551371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.78723.724427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.706151762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2871580
X-RAY DIFFRACTIONr_chiral_restr0.0620.21670
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022090
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_it0.4031.56775
X-RAY DIFFRACTIONr_mcbond_other0.1021.52786
X-RAY DIFFRACTIONr_mcangle_it0.769210782
X-RAY DIFFRACTIONr_scbond_it1.35233738
X-RAY DIFFRACTIONr_scangle_it2.2814.53475
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Number: 4167 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.370.5
2Bmedium positional0.310.5
3Cmedium positional0.30.5
4Dmedium positional0.330.5
1Amedium thermal0.432
2Bmedium thermal0.452
3Cmedium thermal0.362
4Dmedium thermal0.382
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 242 -
Rwork0.233 4259 -
obs-4501 99.54 %
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)
10.91270.0797-0.70330.7908-0.07262.05920.02610.12030.0688-0.28880.02260.1227-0.54-0.0261-0.04870.3293-0.0137-0.05420.0620.00370.0614.893216.1756-2.7154
20.83380.0461-0.10231.53670.32751.8661-0.0309-0.00150.181-0.1793-0.00340.173-0.6844-0.03720.03430.3390.0115-0.0530.03620.00270.110713.143623.771811.1042
31.30570.56040.3310.78540.15580.58650.0167-0.10760.09140.0821-0.04850.0482-0.08-0.0480.03180.0338-0.02070.00960.071-0.0240.041930.650120.884152.1771
40.97310.30930.4190.80020.16480.7711-0.00460.1296-0.0286-0.11610.0197-0.0887-0.08860.0788-0.01510.0429-0.03060.02510.0908-0.02060.062633.88816.104737.7094
50.90250.0606-0.17750.8977-0.47221.50710.0529-0.12570.02210.1875-0.05260.06370.0273-0.1062-0.00030.0654-0.05780.02860.1093-0.0490.03261.3889-1.575261.1779
60.8497-0.11150.17811.03170.10630.80510.0308-0.0280.00490.0517-0.09040.16090.0323-0.12790.05970.0166-0.0410.02360.1119-0.05370.0878-6.5691-1.728747.5027
70.60030.2264-0.09741.43430.34191.4687-0.05980.13050.0507-0.20160.01120.14310.0759-0.20890.04860.0545-0.0084-0.0350.09180.00120.03830.3951-17.50015.6469
80.58480.34510.01561.44810.11431.1548-0.0296-0.0553-0.04560.01180.002-0.02950.1109-0.02670.02750.01350.00540.00180.04570.00950.04616.0367-19.798520.043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 127
2X-RAY DIFFRACTION2A128 - 338
3X-RAY DIFFRACTION3B0 - 127
4X-RAY DIFFRACTION4B128 - 338
5X-RAY DIFFRACTION5C0 - 127
6X-RAY DIFFRACTION6C128 - 339
7X-RAY DIFFRACTION7D0 - 127
8X-RAY DIFFRACTION8D128 - 339

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