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- PDB-3oce: Crystal structure of fumarate lyase:delta crystallin from Brucell... -

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Basic information

Entry
Database: PDB / ID: 3oce
TitleCrystal structure of fumarate lyase:delta crystallin from Brucella melitensis bound to cobalt
ComponentsFumarate lyase:Delta crystallin
KeywordsLYASE / fumarate lyase / fumarase / brucellosis / orchitis / epididymitis / mastitis / dehydration of fumarate to malate / Kreb's cycle / citric acid cycle / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


aspartate ammonia-lyase / aspartate ammonia-lyase activity / tricarboxylic acid cycle
Similarity search - Function
: / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...: / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Fumarate lyase:Delta crystallin
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.58 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of fumarate lyase:delta crystallin from Brucella melitensis bound to cobalt
Authors: Edwards, T.E. / Arakaki, T.L. / Sankaran, B.
History
DepositionAug 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2019Group: Database references / Derived calculations
Category: pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.3Sep 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_ncs_dom_lim / 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.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.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_conn.ptnr2_label_seq_id / _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_ncs_dom_lim.end_label_seq_id / _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: Fumarate lyase:Delta crystallin
B: Fumarate lyase:Delta crystallin
C: Fumarate lyase:Delta crystallin
D: Fumarate lyase:Delta crystallin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,80321
Polymers203,8924
Non-polymers91117
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31240 Å2
ΔGint-269 kcal/mol
Surface area55720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.330, 113.550, 236.860
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C

NCS domain segments:

Component-ID: 1 / Refine code: 5

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETILEILEAA1 - 4055 - 409
21METMETILEILEBB1 - 4055 - 409
31METMETILEILECC1 - 4055 - 409
41METMETILEILEDD1 - 4055 - 409
12SERSERALAALAAA406 - 458410 - 462
22SERSERALAALABB406 - 458410 - 462
32SERSERALAALACC406 - 458410 - 462

NCS ensembles :
ID
1
2

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Components

#1: Protein
Fumarate lyase:Delta crystallin


Mass: 50973.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 2308 / Gene: aspA, BAB1_1959 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2YLW1, aspartate ammonia-lyase
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Co
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 46.3 mg/mL BrabA.00047.a.A6 PS00513 against JCSG+ condition G3, 10 mM CoCl2, 0.1 M Tris, 20% polyvinyl pyrrolidone K15 with 20% ethylene glycol as cryo-protectant, crsytal tracking ID ...Details: 46.3 mg/mL BrabA.00047.a.A6 PS00513 against JCSG+ condition G3, 10 mM CoCl2, 0.1 M Tris, 20% polyvinyl pyrrolidone K15 with 20% ethylene glycol as cryo-protectant, crsytal tracking ID 215219g3, 3C protease cleaved, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→50 Å / Num. all: 81644 / Num. obs: 80944 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 29.903 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 10.03
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.58-2.650.5653.135260588699
2.65-2.720.5013.635293572899
2.72-2.80.4334.135297562298.8
2.8-2.880.3864.634738543599.3
2.88-2.980.3275.534756532099.1
2.98-3.080.294634402515399.5
3.08-3.20.251733816492199.2
3.2-3.330.218.433309475798.9
3.33-3.480.1759.932799458299.5
3.48-3.650.1511.332517443099.4
3.65-3.850.12613.531300417399.6
3.85-4.080.10914.830594397799.7
4.08-4.360.09516.929681380199.9
4.36-4.710.08717.927530349099.9
4.71-5.160.08817.125800325699.9
5.16-5.770.10115.9258152935100
5.77-6.660.09516231402639100
6.66-8.160.06619.8195402249100
8.16-11.540.04924.915114177099.9
11.540.04224.4668082078.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.67 Å19.95 Å
Translation2.67 Å19.95 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1jsw

1jsw


Resolution: 2.58→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / WRfactor Rfree: 0.2158 / WRfactor Rwork: 0.1707 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.773 / SU B: 20.838 / SU ML: 0.203 / SU R Cruickshank DPI: 0.4471 / SU Rfree: 0.2799 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.28 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 4054 5 %RANDOM
Rwork0.1959 ---
obs0.1984 80691 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 76.49 Å2 / Biso mean: 29.6871 Å2 / Biso min: 3.83 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å20 Å20 Å2
2---0.06 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.58→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13775 0 20 544 14339
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02214000
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.97219021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.79351846
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.2224.223592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.128152344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.415115
X-RAY DIFFRACTIONr_chiral_restr0.1040.22280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110511
X-RAY DIFFRACTIONr_mcbond_it0.6241.59168
X-RAY DIFFRACTIONr_mcangle_it1.227214683
X-RAY DIFFRACTIONr_scbond_it1.99934832
X-RAY DIFFRACTIONr_scangle_it3.5584.54334
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1617MEDIUM POSITIONAL0.20.5
12B1617MEDIUM POSITIONAL0.170.5
13C1617MEDIUM POSITIONAL0.230.5
14D1617MEDIUM POSITIONAL0.170.5
11A1393LOOSE POSITIONAL0.415
12B1393LOOSE POSITIONAL0.385
13C1393LOOSE POSITIONAL0.465
14D1393LOOSE POSITIONAL0.365
11A1617MEDIUM THERMAL0.612
12B1617MEDIUM THERMAL0.62
13C1617MEDIUM THERMAL0.682
14D1617MEDIUM THERMAL0.62
11A1393LOOSE THERMAL0.8210
12B1393LOOSE THERMAL0.8110
13C1393LOOSE THERMAL0.8610
14D1393LOOSE THERMAL0.7810
21A212MEDIUM POSITIONAL0.180.5
22B212MEDIUM POSITIONAL0.150.5
23C212MEDIUM POSITIONAL0.270.5
21A144LOOSE POSITIONAL0.45
22B144LOOSE POSITIONAL0.435
23C144LOOSE POSITIONAL0.735
21A212MEDIUM THERMAL0.432
22B212MEDIUM THERMAL0.362
23C212MEDIUM THERMAL0.532
21A144LOOSE THERMAL0.5510
22B144LOOSE THERMAL0.4510
23C144LOOSE THERMAL0.6910
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 314 -
Rwork0.257 5550 -
all-5864 -
obs--98.85 %
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)
1-0.030.0777-0.15490.0881-0.05240.23230.0349-0.00840.01480.0032-0.0157-0.0090.00620.0077-0.01910.01570.0063-0.00010.0264-0.00710.025-6.9863-16.094810.4914
2-0.02050.0840.12580.08980.0380.11550.033-0.00880.00030.0042-0.0337-0.00810.0024-0.00490.00070.02230.0076-0.00010.0322-0.01010.039410.725516.110110.8276
30.0084-0.0680.09060.15560.06330.22830.00270.0173-0.00240.0526-0.01560.0582-0.02920.01680.01290.00890.00230.00320.0515-0.01240.0678-14.37128.974218.0934
4-0.0385-0.0897-0.04610.0904-0.0870.14310.0040.01560.01710.0442-0.0255-0.07410.0134-0.02760.02150.0234-0.0141-0.00020.05390.00050.068217.9114-9.335118.0304
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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