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- PDB-4lw8: Crystal structure of a putative epimerase from Burkholderia cenoc... -

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Basic information

Entry
Database: PDB / ID: 4lw8
TitleCrystal structure of a putative epimerase from Burkholderia cenocepacia J2315
ComponentsPutative epimerase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / putative epimerase
Function / homology
Function and homology information


GDP-mannose 4,6 dehydratase / NAD(P)-binding domain / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a putative epimerase from Burkholderia cenocepacia J2315
Authors: Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Sep 20, 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_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_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: Putative epimerase
B: Putative epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4814
Polymers71,0052
Non-polymers4772
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-8 kcal/mol
Surface area25990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.970, 98.970, 173.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain: (Details: CHAIN B) / NCS domain segments: (Selection details: CHAIN B)

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Components

#1: Protein Putative epimerase


Mass: 35502.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / LMG 16656 / Gene: BCAM1003, BceJ2315_44580 / Plasmid: BuceA.00050.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4EFL1
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: EmeraldBio JCSG screen c4: 10% PEG 600, 100mM HEPES, pH 7.5, cryo protected with 15% EG. BuceA.00050.a.B1.PS01171 at 23.6 mg/ml, tray 246217, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 2, 2013
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 58166 / Num. obs: 57752 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.95 % / Biso Wilson estimate: 31.39 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 21.2
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.1-2.150.5123.532624042281100
2.15-2.210.4654.02251594112199.9
2.21-2.280.3356.1192583693191.2
2.28-2.350.296.26239563939199.9
2.35-2.420.2267.892321437391100
2.42-2.510.1729.972297136891100
2.51-2.60.13712.462211635691100
2.6-2.710.11215.242104234161100
2.71-2.830.0918.472037032921100
2.83-2.970.07421.771914431311100
2.97-3.130.05826.841835930211100
3.13-3.320.04831.931709928501100
3.32-3.550.04237.131555126731100
3.55-3.830.03938.67133482503199.6
3.83-4.20.03443.99127732302199.9
4.2-4.70.02949.591214421301100
4.7-5.420.02849.211065318631100
5.42-6.640.02649.56932616121100
6.64-9.390.02153.85714712591100
9.39-500.0254.243731731195.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å19.87 Å
Translation3.5 Å19.87 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIXdev_1439refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2pk3, modified with CCP4 program chainsaw

2pk3


Resolution: 2.1→32.628 Å / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8487 / SU ML: 0.22 / Isotropic thermal model: isotropic, TLS / σ(F): 1.36 / Phase error: 21.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2097 2926 5.08 %random
Rwork0.1766 ---
obs0.1782 57649 99.24 %-
all-58166 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.87 Å2 / Biso mean: 39.2726 Å2 / Biso min: 13.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.628 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4461 0 30 371 4862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084634
X-RAY DIFFRACTIONf_angle_d1.0226348
X-RAY DIFFRACTIONf_chiral_restr0.044746
X-RAY DIFFRACTIONf_plane_restr0.005825
X-RAY DIFFRACTIONf_dihedral_angle_d11.9291679
Refine LS restraints NCSNumber: 2580 / Type: POSITIONAL / Rms dev position: 3.963 Å
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13450.29331470.230125402687100
2.1345-2.17130.29461520.227925942746100
2.1713-2.21070.27981510.235925572708100
2.2107-2.25330.49971190.44782372249190
2.2533-2.29920.32551320.29972469260195
2.2992-2.34920.24511340.205626132747100
2.3492-2.40380.22991400.182225682708100
2.4038-2.46390.21971520.167525932745100
2.4639-2.53050.21251390.166326022741100
2.5305-2.6050.22161390.162726092748100
2.605-2.6890.19891460.159526092755100
2.689-2.78510.2131300.164525952725100
2.7851-2.89650.23461210.178426482769100
2.8965-3.02830.19751620.169326062768100
3.0283-3.18780.22691460.177826102756100
3.1878-3.38730.21751280.175126422770100
3.3873-3.64850.20641210.174926622783100
3.6485-4.01510.19461330.159326462779100
4.0151-4.59470.1441510.138726552806100
4.5947-5.78360.16041490.144727002849100
5.7836-32.63180.18781340.163128332967100
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)
11.916-0.86340.57253.47860.54384.40830.07610.013-0.15530.4204-0.0251-0.13290.48590.1764-0.05930.2891-0.0121-0.0730.1795-0.02610.2917-11.32467.110616.0277
21.9770.64960.69692.76770.12312.48420.0824-0.00670.00580.1137-0.07880.1646-0.0179-0.1841-0.00380.15560.0096-0.01140.16720.02670.2112-17.267584.050813.2405
33.78381.14422.34812.15091.2692.90920.1056-0.27560.18490.5451-0.1118-0.04720.0377-0.1924-0.03390.3822-0.05250.02740.21350.01430.2165-10.626285.121534.2164
44.5279-0.5438-0.08283.0214-0.95234.19020.14460.606-0.0099-0.2481-0.1535-0.15690.00670.14090.03710.18830.0283-0.0030.25240.00320.1949-2.654107.0514-9.3958
51.78690.1358-0.01433.1659-0.1361.33370.0246-0.0813-0.17840.0289-0.02370.0219-0.0045-0.08980.00510.17030.019-0.04140.18950.01680.1376-13.495598.88223.3966
63.39010.16361.05242.17450.16683.59330.17290.5937-0.3063-0.4205-0.08210.39380.2821-0.3621-0.04040.26470.0503-0.10380.3129-0.05990.255-24.4458104.1196-10.8406
73.2410.11611.07921.90080.38093.6720.0610.5488-0.3163-0.47080.090.48660.206-0.1165-0.12340.30510.0636-0.14270.3701-0.04840.345-29.3718104.4059-13.8611
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 7:94 )A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 95:181 )A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 182:314 )A0
4X-RAY DIFFRACTION4CHAIN B AND (RESID 7:94 )B0
5X-RAY DIFFRACTION5CHAIN B AND (RESID 95:166 )B0
6X-RAY DIFFRACTION6CHAIN B AND (RESID 167:260 )B0
7X-RAY DIFFRACTION7CHAIN B AND (RESID 261:314 )B0

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