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- PDB-4bfc: Crystal structure of the C-terminal CMP-Kdo binding domain of Waa... -

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Basic information

Entry
Database: PDB / ID: 4bfc
TitleCrystal structure of the C-terminal CMP-Kdo binding domain of WaaA from Acinetobacter baumannii
Components3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE
KeywordsTRANSFERASE
Function / homologyGlycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / BETA-MERCAPTOETHANOL / 3-Deoxy-D-manno-octulosonic-acid transferase (Kdotransferase) family protein / :
Function and homology information
Biological speciesACINETOBACTER BAUMANNII (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsKimbung, Y.R. / Hakansson, M. / Logan, D. / Wang, P.F. / Schulz, M. / Mamat, U. / Woodard, R.W.
CitationJournal: To be Published
Title: Crystal Structure of the C-Terminal Cmp-Kdo Binding Domain of Waaa from Acinetobacter Baumannii
Authors: Kimbung, Y.R. / Hakansson, M. / Logan, D. / Wang, P.F. / Schulz, M. / Mamat, U. / Woodard, R.W.
History
DepositionMar 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Structure summary
Revision 1.2Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: 3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0274
Polymers26,7741
Non-polymers2523
Water3,351186
1
A: 3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE
hetero molecules

A: 3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE
hetero molecules

A: 3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,08012
Polymers80,3233
Non-polymers7579
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation2_555-y,x-y,z1
Buried area4530 Å2
ΔGint-50.9 kcal/mol
Surface area24220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.370, 110.370, 70.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein 3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE


Mass: 26774.201 Da / Num. of mol.: 1
Fragment: C-TERMINAL CMP-KDO BINDING DOMAIN, RESIDUES 220-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACINETOBACTER BAUMANNII (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSSETTA2 PLYSS / References: UniProt: K5F2Z1, UniProt: A0A7U4CWN3*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / 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: 64.5 % / Description: NONE
Crystal growpH: 6
Details: 0.1M NA CITRATE BUFFER PH 6.0, 0.2 MM LITHIUM SULPHATE AND 17 TO 23 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.041
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Feb 1, 2012 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.041 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.585
11K, H, -L20.415
ReflectionResolution: 1.7→30 Å / Num. obs: 35057 / % possible obs: 99.4 % / Observed criterion σ(I): 3.77 / Redundancy: 5.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24.9
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3.77 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XCI

2xci


Resolution: 1.7→28.33 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.229 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT SIDE CHAINS WITH POOR ELECTRON DENSITY WERE MODELED WITH ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT SIDE CHAINS WITH POOR ELECTRON DENSITY WERE MODELED WITH LOWER OCCUPANCY. MULTIPLE CONFORMERS WERE MODELED WITH LOWER OCCUPANCY ADDING UP TO 1.
RfactorNum. reflection% reflectionSelection details
Rfree0.16093 1754 5 %RANDOM
Rwork0.13383 ---
obs0.13518 33299 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.23 Å2
Baniso -1Baniso -2Baniso -3
1--9.83 Å20 Å20 Å2
2---9.83 Å20 Å2
3---19.67 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1532 0 13 186 1731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021624
X-RAY DIFFRACTIONr_bond_other_d0.0190.021624
X-RAY DIFFRACTIONr_angle_refined_deg1.8851.9372223
X-RAY DIFFRACTIONr_angle_other_deg1.8851.9372223
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2015206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.17425.17685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.58115264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.105159
X-RAY DIFFRACTIONr_chiral_restr0.1350.2251
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211264
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 132 -
Rwork0.258 2384 -
obs--97.14 %

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