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- PDB-3r4i: Crystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERI... -

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Basic information

Entry
Database: PDB / ID: 3r4i
TitleCrystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERIA XENOVORANS LB400 at 2.24 A resolution
ComponentsCitrate Lyase
KeywordsLYASE / TIM beta/alpha-barrel / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-biology
Function / homology
Function and homology information


citrate (pro-3S)-lyase / citrate (pro-3S)-lyase activity / regulation of cobalamin metabolic process / (S)-citramalyl-CoA lyase activity / metal ion binding
Similarity search - Function
Helix Hairpins - #960 / Citramalyl-CoA lyase / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Helix Hairpins / Helix non-globular / Special ...Helix Hairpins - #960 / Citramalyl-CoA lyase / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / Helix Hairpins / Helix non-globular / Special / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.24 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Citrate lyase (Bxe_B2899) from BURKHOLDERIA XENOVORANS LB400 at 2.24 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citrate Lyase
B: Citrate Lyase
C: Citrate Lyase
D: Citrate Lyase
E: Citrate Lyase
F: Citrate Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,01726
Polymers225,2016
Non-polymers81620
Water5,152286
1
A: Citrate Lyase
hetero molecules

A: Citrate Lyase
hetero molecules

A: Citrate Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,8419
Polymers112,6003
Non-polymers2406
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10320 Å2
ΔGint-107 kcal/mol
Surface area35430 Å2
MethodPISA
2
B: Citrate Lyase
hetero molecules

B: Citrate Lyase
hetero molecules

B: Citrate Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,94712
Polymers112,6003
Non-polymers3479
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area10780 Å2
ΔGint-139 kcal/mol
Surface area35010 Å2
MethodPISA
3
C: Citrate Lyase
hetero molecules

C: Citrate Lyase
hetero molecules

C: Citrate Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,12415
Polymers112,6003
Non-polymers52412
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area12060 Å2
ΔGint-175 kcal/mol
Surface area34770 Å2
MethodPISA
4
D: Citrate Lyase
hetero molecules

D: Citrate Lyase
hetero molecules

D: Citrate Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,24518
Polymers112,6003
Non-polymers64415
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11540 Å2
ΔGint-145 kcal/mol
Surface area33480 Å2
MethodPISA
5
E: Citrate Lyase
hetero molecules

E: Citrate Lyase
hetero molecules

E: Citrate Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,94712
Polymers112,6003
Non-polymers3479
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area10370 Å2
ΔGint-148 kcal/mol
Surface area34190 Å2
MethodPISA
6
F: Citrate Lyase
hetero molecules

F: Citrate Lyase
hetero molecules

F: Citrate Lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,94712
Polymers112,6003
Non-polymers3479
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area10440 Å2
ΔGint-149 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.468, 148.468, 79.570
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

21C-577-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 4:12 or resseq 17:327 )A4 - 12
121chain A and (resseq 4:12 or resseq 17:327 )A17 - 327
211chain B and (resseq 4:12 or resseq 17:327 )B4 - 12
221chain B and (resseq 4:12 or resseq 17:327 )B17 - 327
311chain C and (resseq 4:12 or resseq 17:327 )C4 - 12
321chain C and (resseq 4:12 or resseq 17:327 )C17 - 327
411chain D and (resseq 4:12 or resseq 17:327 )D4 - 12
421chain D and (resseq 4:12 or resseq 17:327 )D17 - 327
511chain E and (resseq 4:12 or resseq 17:327 )E4 - 12
521chain E and (resseq 4:12 or resseq 17:327 )E17 - 327
611chain F and (resseq 4:12 or resseq 17:327 )F4 - 12
621chain F and (resseq 4:12 or resseq 17:327 )F17 - 327
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein
Citrate Lyase


Mass: 37533.438 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: Bxeno_B0128, Bxe_B2899 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13S43, citrate (pro-3S)-lyase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.25 Å3/Da / Density % sol: 45.29 %
Description: THE STRUCTURE WAS INITIALLY PHASED IN SPACE GROUP P321. HOWEVER, ANAYSIS OF THE SOLUTION USING XTRIAGE AND INITIAL REFINEMENT RESULTS SUGGESTED THAT THE CORRECT SPACE GROUP WAS P3 WITH MEROHEDRAL TWINNING.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.33
Details: 44.0% polyethylene glycol 600, 0.15M calcium acetate, 0.1M sodium cacodylate pH 6.33, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97879
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 10, 2010
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97879 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.476
ReflectionResolution: 2.24→48.598 Å / Num. obs: 93682 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 37.127 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.36
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.24-2.320.5271.8357061812796
2.32-2.410.3772.4346491754096
2.41-2.520.3093364241842696.7
2.52-2.650.253.6354761793796.5
2.65-2.820.175.2370571874797.1
2.82-3.040.1217.3365881850197.1
3.04-3.340.06912358331811897.2
3.34-3.820.03720.6362561834496.9
3.82-4.810.02430.2364691845397.4
4.810.01936.7366321856097.3

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 30, 2009data scaling
PHENIX1.6.4refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.24→48.598 Å / Occupancy max: 1 / Occupancy min: 0.33 / σ(F): 1.71 / Stereochemistry target values: TWIN_LSQ_F
Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. CALCIUM (CA) AND ACETATE (ACT) FROM THE CRYSTALLIZATION SOLUTION, AND CHLORIDE (CL) FROM THE PURIFICATION BUFFER WERE MODELED INTO THE STRUCTURE. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. THE DIFFRACTION DATA SHOW MEROHEDERAL TWINNING WITH TWIN LAW "H, -H-K, -L". THE REFINED TWIN FRACTION WAS 0.48. THE R-FREE TEST SET REFLECTIONS WERE CHOSEN AT RANDOM WITH THE TWIN LAW INCLUDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1737 4707 5.02 %RANDOM + TWIN LAW
Rwork0.1513 ---
obs0.1532 93681 99.28 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.443 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 110.84 Å2 / Biso mean: 37.4499 Å2 / Biso min: 4.77 Å2
Baniso -1Baniso -2Baniso -3
1-3.5924 Å2-0 Å2-0 Å2
2--3.5924 Å2-0 Å2
3----7.1847 Å2
Refinement stepCycle: LAST / Resolution: 2.24→48.598 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14387 0 26 286 14699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714875
X-RAY DIFFRACTIONf_angle_d0.95620355
X-RAY DIFFRACTIONf_chiral_restr0.0642323
X-RAY DIFFRACTIONf_plane_restr0.0042687
X-RAY DIFFRACTIONf_dihedral_angle_d11.2865190
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2374X-RAY DIFFRACTIONPOSITIONAL0.041
12B2374X-RAY DIFFRACTIONPOSITIONAL0.041
13C2375X-RAY DIFFRACTIONPOSITIONAL0.04
14D2375X-RAY DIFFRACTIONPOSITIONAL0.032
15E2315X-RAY DIFFRACTIONPOSITIONAL0.04
16F2327X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2404-2.2790.252140.2244423463793
2.279-2.32040.24862510.21554465471694
2.3204-2.3650.23362110.20254395460694
2.365-2.41330.25122570.19774385464293
2.4133-2.46570.212250.19464473469895
2.4657-2.52310.21292250.19094455468094
2.5231-2.58620.20841990.18974500469995
2.5862-2.65610.22072500.18884412466294
2.6561-2.73420.17862120.17914437464995
2.7342-2.82240.21152380.17354477471595
2.8224-2.92320.20232580.17764437469594
2.9232-3.04020.2082200.17834425464595
3.0402-3.17840.19212410.17014486472794
3.1784-3.34590.17512370.15754434467194
3.3459-3.55530.17282650.14294418468394
3.5553-3.82940.16662360.13284480471694
3.8294-4.21420.13452350.11254452468795
4.2142-4.82240.12532440.1084463470795
4.8224-6.06990.13392420.12314463470595
6.0699-33.64110.16592410.14054453469494
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)
10.39350.0564-0.09770.28010.06710.20440.01690.0767-0.0004-0.0427-0.0167-0.04890.02160.049100.10850.04250.02880.14270.01240.109214.6352-17.8845-34.2697
20.0479-0.01580.04450.0316-0.03830.0605-0.0630.0552-0.2038-0.02960.0669-0.01110.252-0.080300.1694-0.02470.02040.1299-0.03430.2387-16.4538-26.0585-24.5067
30.2838-0.13370.0380.1576-0.19210.32670.0279-0.0760.0250.0398-0.00080.03990.1276-0.032500.1633-0.01660.03150.06390.0140.0819-4.3929-22.62029.9398
40.0384-0.01470.00010.03410.03930.04890.0042-0.0552-0.0908-0.06540.0251-0.12830.0950.1515-00.16230.05020.00470.16860.0640.206126.9988-15.04050.1446
50.3274-0.05570.17960.2252-0.19150.3379-0.05560.067-0.055-0.03140.0778-0.04960.122-0.18900.1801-0.0492-0.00370.2229-0.02140.126156.7195-57.972617.7809
60.0403-0.0279-0.01120.0326-0.02190.05850.13630.0617-0.04340.0975-0.19570.1694-0.2293-0.0032-0.00010.26060.1045-0.03130.30250.03930.239247.9587-27.172927.7626
70.2054-0.0733-0.08780.283-0.11870.2401-0.0316-0.0221-0.0201-0.01290.0456-0.0097-0.0722-0.050100.0570.00880.01960.1442-0.01010.125251.4073-38.8984-17.7805
80.0331-0.03710.03460.045-0.02950.08140.04750.134-0.0683-0.1778-0.00680.0031-0.15050.0517-00.1578-0.06940.02510.1215-0.00750.111159.7418-69.911-27.3859
90.1382-0.06170.00840.1462-0.01770.2627-0.04830.08560.0637-0.04780.00360.007-0.09920.1944-00.1304-0.0498-0.03440.1440.05010.140313.0723-66.791725.2325
100.0679-0.0156-0.03590.01510.00840.0177-0.0419-0.0230.05880.20880.1339-0.14110.0654-0.061100.16760.04130.0250.25010.05150.227429.7827-93.98634.6508
110.21780.2587-0.0180.43380.04960.208-0.0008-0.181-0.08150.1016-0.0889-0.0623-0.05030.1604-00.21220.0066-0.06040.36260.08260.176423.036-83.8572-10.5191
120.0301-0.0218-0.0160.02240.02790.0345-0.0934-0.0330.28390.0173-0.0261-0.1561-0.081-0.1369-00.26510.0024-0.0980.1777-0.04260.13177.2535-55.7763-19.984
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:266)A3 - 266
2X-RAY DIFFRACTION2(chain A and resid 267:327)A267 - 327
3X-RAY DIFFRACTION3(chain B and resid 3:266)B3 - 266
4X-RAY DIFFRACTION4(chain B and resid 267:327)B267 - 327
5X-RAY DIFFRACTION5(chain C and resid 4:266)C4 - 266
6X-RAY DIFFRACTION6(chain C and resid 267:327)C267 - 327
7X-RAY DIFFRACTION7(chain D and resid 4:266)D4 - 266
8X-RAY DIFFRACTION8(chain D and resid 267:327)D267 - 327
9X-RAY DIFFRACTION9(chain E and resid 2:266)E2 - 266
10X-RAY DIFFRACTION10(chain E and resid 267:328)E267 - 328
11X-RAY DIFFRACTION11(chain F and resid 4:266)F4 - 266
12X-RAY DIFFRACTION12(chain F and resid 267:327)F267 - 327

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Yorodumi

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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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