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Entry
Database: PDB / ID: 4nav
TitleCrystal structure of hypothetical protein XCC2798 from Xanthomonas campestris, Target EFI-508608
ComponentsHYPOTHETICAL PROTEIN XCC279
KeywordsHYDROLASE / Structural Genomics / Enzyme Function Initiative
Function / homology
Function and homology information


3-deoxy-manno-octulosonate-8-phosphatase activity / 3-deoxy-manno-octulosonate-8-phosphatase / lipopolysaccharide biosynthetic process / metal ion binding
Similarity search - Function
KdsC family / : / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-deoxy-D-manno-octulosonate 8-phosphate phosphatase KdsC
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsKim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Glenn, A.S. / Chowdhury, S. ...Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Glenn, A.S. / Chowdhury, S. / Evans, B. / Zhao, S.C. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Stead, M. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of hypothetical protein XCC2798 from Xanthomonas campestris, Target EFI-508608
Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Zhao, S. / Hillerich, B. / ...Authors: Kim, J. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Zhao, S. / Hillerich, B. / Love, J. / Seidel, R.D. / Imker, H.J. / Stead, M. / Jacobson, M.P. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / 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
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_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: HYPOTHETICAL PROTEIN XCC279
A: HYPOTHETICAL PROTEIN XCC279
B: HYPOTHETICAL PROTEIN XCC279
C: HYPOTHETICAL PROTEIN XCC279


Theoretical massNumber of molelcules
Total (without water)78,2694
Polymers78,2694
Non-polymers00
Water66737
1
D: HYPOTHETICAL PROTEIN XCC279
C: HYPOTHETICAL PROTEIN XCC279

D: HYPOTHETICAL PROTEIN XCC279
C: HYPOTHETICAL PROTEIN XCC279


Theoretical massNumber of molelcules
Total (without water)78,2694
Polymers78,2694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9880 Å2
ΔGint-43 kcal/mol
Surface area26400 Å2
MethodPISA
2
A: HYPOTHETICAL PROTEIN XCC279
B: HYPOTHETICAL PROTEIN XCC279

A: HYPOTHETICAL PROTEIN XCC279
B: HYPOTHETICAL PROTEIN XCC279


Theoretical massNumber of molelcules
Total (without water)78,2694
Polymers78,2694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area9580 Å2
ΔGint-45 kcal/mol
Surface area26230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.903, 156.017, 111.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21A
12D
22B
13D
23C
14A
24B
15A
25C
16B
26C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROSERSERDA2 - 1812 - 181
21PROPROSERSERAB2 - 1812 - 181
12METMETPHEPHEDA1 - 1801 - 180
22METMETPHEPHEBC1 - 1801 - 180
13METMETALAALADA1 - 1821 - 182
23METMETALAALACD1 - 1821 - 182
14PROPROPHEPHEAB2 - 1802 - 180
24PROPROPHEPHEBC2 - 1802 - 180
15PROPROSERSERAB2 - 1812 - 181
25PROPROSERSERCD2 - 1812 - 181
16METMETPHEPHEBC1 - 1801 - 180
26METMETPHEPHECD1 - 1801 - 180

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
HYPOTHETICAL PROTEIN XCC279


Mass: 19567.291 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: ATCC 33913 / Gene: XCC2798 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8P716
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 85mM Tris-HCl, pH 8.5 0.17M sodium acetate 25.5% PEG4000,15% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: RAYONIX MX325HE / Detector: CCD / Date: Oct 12, 2013
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.69→111.51 Å / Num. all: 21987 / Num. obs: 21866 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 17.2
Reflection shellResolution: 2.69→2.83 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3145 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.8.0049refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3N1U

3n1u


Resolution: 2.69→78.01 Å / Cor.coef. Fo:Fc: 0.874 / Cor.coef. Fo:Fc free: 0.852 / SU B: 32.272 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1095 5.2 %RANDOM
Rwork0.24358 ---
obs0.24516 20128 96.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.199 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2--1.68 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.69→78.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5331 0 0 37 5368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195427
X-RAY DIFFRACTIONr_bond_other_d0.0060.025188
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9627396
X-RAY DIFFRACTIONr_angle_other_deg1.196311827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4495722
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.20123.932234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.60915804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1131541
X-RAY DIFFRACTIONr_chiral_restr0.080.2858
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216354
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021227
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_it1.4892.5012900
X-RAY DIFFRACTIONr_mcbond_other1.4892.5012899
X-RAY DIFFRACTIONr_mcangle_it2.4473.7483618
X-RAY DIFFRACTIONr_mcangle_other2.4473.7483619
X-RAY DIFFRACTIONr_scbond_it1.8622.6362527
X-RAY DIFFRACTIONr_scbond_other1.8612.6362528
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0393.883779
X-RAY DIFFRACTIONr_long_range_B_refined4.51519.3915798
X-RAY DIFFRACTIONr_long_range_B_other4.51519.3925799
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D100280.08
12A100280.08
21D97920.09
22B97920.09
31D96940.1
32C96940.1
41A98930.08
42B98930.08
51A97700.11
52C97700.11
61B98220.09
62C98220.09
LS refinement shellResolution: 2.688→2.758 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 90 -
Rwork0.316 1490 -
obs--99.5 %
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)
11.03-0.36411.30190.8449-0.34162.34940.24190.0589-0.0791-0.03710.04980.08510.37040.1643-0.29180.16420.0322-0.15410.07240.01190.2567-6.337321.87547.4112
22.3568-0.3186-0.45230.41410.13051.18110.26890.24210.63280.023-0.0588-0.0118-0.19380.021-0.21010.230.04260.29980.04860.12160.526810.658264.36659.0753
31.74820.04661.19651.23890.82772.61210.12030.07160.5933-0.0188-0.1190.1005-0.2059-0.1871-0.00130.18520.06610.24260.03950.09530.4646-18.893764.209816.959
42.3466-0.90490.09690.7306-0.05472.88480.1594-0.3127-0.2764-0.11940.03720.11860.2903-0.6983-0.19660.1516-0.1001-0.16560.23720.0880.2376-20.832621.420834.3147
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D1 - 182
2X-RAY DIFFRACTION2A2 - 182
3X-RAY DIFFRACTION3B1 - 181
4X-RAY DIFFRACTION4C1 - 182

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