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- PDB-3pm6: Crystal structure of a putative fructose-1,6-biphosphate aldolase... -

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Basic information

Entry
Database: PDB / ID: 3pm6
TitleCrystal structure of a putative fructose-1,6-biphosphate aldolase from Coccidioides immitis solved by combined SAD MR
ComponentsPutative fructose-bisphosphate aldolase
KeywordsLYASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / coccidioidomycosis / Coccidioides / Valley Fever / immitis / posadasii / fructose-1 / 6-bisphosphate aldolase / zinc-containing enzyme / pathogenic fungus
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Putative fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / SAD WITH molecular replacement / SAD / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: J Struct Funct Genomics / Year: 2011
Title: SAD phasing using iodide ions in a high-throughput structural genomics environment.
Authors: Abendroth, J. / Gardberg, A.S. / Robinson, J.I. / Christensen, J.S. / Staker, B.L. / Myler, P.J. / Stewart, L.J. / Edwards, T.E.
History
DepositionNov 16, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Putative fructose-bisphosphate aldolase
B: Putative fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,77737
Polymers67,4592
Non-polymers4,31935
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint-99 kcal/mol
Surface area19940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.910, 77.770, 68.320
Angle α, β, γ (deg.)90.000, 93.710, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A5 - 298
2116B5 - 298

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Components

#1: Protein Putative fructose-bisphosphate aldolase / / FBP aldolase / FBPA / Putative fructose-1 / 6-bisphosphate aldolase


Mass: 33729.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Gene: CIMG_05755 / Production host: Escherichia coli (E. coli) / References: UniProt: P0CJ44, fructose-bisphosphate aldolase
#2: Chemical...
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 33 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.28 Å3/Da / Density % sol: 45.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 23.4 mg/mL CoimA.00345.a.A1 PS00465 against ProPlex screen condition E11, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, soaked into 1 M NaI, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, 20% ...Details: 23.4 mg/mL CoimA.00345.a.A1 PS00465 against ProPlex screen condition E11, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, soaked into 1 M NaI, 0.1 M sodium citrate pH 5.0, 20% PEG 8000, 20% ethylene glycol, crystal tracking ID 206915e11, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 14, 2010 / Details: Osmic VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 156341 / Rmerge(I) obs: 0.064 / D res high: 2.5 Å / Num. obs: 40641 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
11.185042693.810.037
7.9111.1884999.610.038
6.457.91106699.210.043
5.596.45130099.810.043
55.59147999.610.04
4.565158599.210.037
4.234.56171998.710.038
3.954.23189199.310.041
3.733.95197298.610.042
3.543.73210499.410.046
3.373.54223898.910.054
3.233.3722539910.072
3.13.2324569910.083
2.993.125129910.103
2.892.99260698.710.122
2.82.89266198.410.141
2.712.8274897.810.165
2.642.71284698.410.196
2.562.64292997.810.227
2.52.56300198.510.26
ReflectionResolution: 2.2→50 Å / Num. all: 30826 / Num. obs: 30048 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 34.628 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 12.96
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.2-2.2660.4783.7112272254186682.8
2.26-2.320.4624.314877213796.6
2.32-2.390.417515483208197.7
2.39-2.460.3615.615392205798
2.46-2.540.2926.714911199798.3
2.54-2.630.2637.314555194898.5
2.63-2.730.2198.513751183698.5
2.73-2.840.1799.813580180598.5
2.84-2.970.14811.613074174398.9
2.97-3.110.1221312387164698.6
3.11-3.280.09815.611774156299.5
3.28-3.480.0818.511427152099.5
3.48-3.720.06222.310553140599.4
3.72-4.020.05923.89955132999.6
4.02-4.40.05525.38971119899.5
4.4-4.920.05726.48248110599.7
4.92-5.680.07124.9733498099.8
5.68-6.960.08324.6601883199.8
6.96-9.840.0728.3461865299.7
9.840.06729.5238035095.6

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.5 Å / D res low: 28.89 Å / FOM : 0.457 / FOM acentric: 0.467 / FOM centric: 0.273 / Reflection: 20866 / Reflection acentric: 19748 / Reflection centric: 961
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8.83-10.570.5850.6130.35220818622
7.74-8.830.5750.590.43623621123
6.97-7.740.5920.6130.41726724026
6.4-6.970.5820.590.46829226723
5.94-6.40.5740.5980.29832029425
5.57-5.940.5540.5740.32333130525
5.27-5.570.5580.5720.31535333218
5-5.270.5580.5710.40538335329
4.78-50.5460.5670.21939436923
4.58-4.780.5450.5570.32640738520
4.4-4.580.4970.5220.24142839127
4.25-4.40.5070.520.25443640922
4.11-4.250.4980.5090.30644642022
3.98-4.110.4950.510.25348445025
3.86-3.980.4830.4950.2547444920
3.76-3.860.490.5110.20752048429
3.66-3.760.4890.5020.21450547821
3.57-3.660.4690.4910.12752349127
3.48-3.570.4710.4860.16854151322
3.4-3.480.4620.4720.26255953323
3.33-3.40.4680.4820.2255052225
3.26-3.330.4880.4980.23857855720
3.19-3.260.4570.4680.21759055926
3.13-3.190.4310.4410.20460457724
3.07-3.130.4590.470.20459657123
3.02-3.070.4270.4360.21262459724
2.97-3.020.4160.4260.16661859322
2.92-2.970.4140.4240.18365763120
2.87-2.920.410.420.19163460726
2.83-2.870.4170.4230.23466964422
2.78-2.830.4060.4130.23465262522
2.74-2.780.4120.4190.22968065621
2.7-2.740.3890.3970.2569466128
2.67-2.70.3960.4020.22371169119
2.63-2.670.4010.4080.23267864921
2.6-2.630.4020.4130.19674971232
2.56-2.60.3970.4020.28372269517
2.53-2.560.3840.3870.33669366423
2.5-2.530.3490.3550.22677974626

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASEREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: SAD WITH molecular replacement
Starting model: 2isv

2isv


Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.912 / WRfactor Rfree: 0.2256 / WRfactor Rwork: 0.1923 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8436 / SU B: 10.248 / SU ML: 0.137 / SU R Cruickshank DPI: 0.2837 / SU Rfree: 0.2101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1505 5 %RANDOM
Rwork0.1978 ---
obs0.1998 30008 97.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.1 Å2 / Biso mean: 27.6569 Å2 / Biso min: 4.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å21.32 Å2
2---0.76 Å20 Å2
3---1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4114 0 35 247 4396
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224191
X-RAY DIFFRACTIONr_angle_refined_deg1.4281.9585702
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5065547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49624.012172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.99815658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9281527
X-RAY DIFFRACTIONr_chiral_restr0.0940.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213150
X-RAY DIFFRACTIONr_mcbond_it0.7081.52747
X-RAY DIFFRACTIONr_mcangle_it1.29824384
X-RAY DIFFRACTIONr_scbond_it2.1131444
X-RAY DIFFRACTIONr_scangle_it3.4254.51317
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1892 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.295
LOOSE THERMAL6.0110
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 89 -
Rwork0.224 1771 -
all-1860 -
obs--82.67 %
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)
10.69590.0322-0.12920.5922-0.00450.36520.0223-0.03170.01050.069-0.0031-0.00050.00730.0519-0.01920.02440.0022-0.01040.0060.00040.0377-21.91061.698566.1561
21.10.10140.12180.376-0.10750.3593-0.0420.17780.0584-0.03940.0283-0.07520.0310.01230.01370.0219-0.00580.01110.0552-0.00490.02595.71142.704738.9796
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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