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- PDB-3ixc: Crystal structure of hexapeptide transferase family protein from ... -

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Basic information

Entry
Database: PDB / ID: 3ixc
TitleCrystal structure of hexapeptide transferase family protein from Anaplasma phagocytophilum
ComponentsHexapeptide transferase family protein
KeywordsTRANSFERASE / NIAID / SSGCID / Seattle Structural Genomics Center for Infectious Disease / gram-negative bacteria / human granulocytic anaplasmosis / beta helix
Function / homology
Function and homology information


transferase activity / metal ion binding
Similarity search - Function
: / : / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Hexapeptide transferase family protein
Similarity search - Component
Biological speciesAnaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.61 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of hexapeptide transferase family protein from Anaplasma phagocytophilum
Authors: Edwards, T.E. / Davies, D.R. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 3, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 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_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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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

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Assembly

Deposited unit
A: Hexapeptide transferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5742
Polymers20,5501
Non-polymers241
Water3,513195
1
A: Hexapeptide transferase family protein
hetero molecules

A: Hexapeptide transferase family protein
hetero molecules

A: Hexapeptide transferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,7226
Polymers61,6493
Non-polymers733
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area4760 Å2
ΔGint-49 kcal/mol
Surface area18120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.091, 92.091, 92.091
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-262-

HOH

21A-268-

HOH

31A-307-

HOH

41A-347-

HOH

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Components

#1: Protein Hexapeptide transferase family protein


Mass: 20549.535 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma phagocytophilum (agent of human granulocytic ehrlichiosis)
Strain: HZ / Gene: APH_1197 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2GIS1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE METAL ION AT RESIDUE 171 IN CHAIN A IS UNKNOWN BUT SUSPECTED TO BE MG2+ BASED ON SOME EVIDENCE.

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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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Hampton CSHT condition D12, 2.0 M ammonium phosphate, 0.1 M Tris pH 8.5, 26.5 mg/mL protein, crystal tracking ID 204803d12, expression tag not removed prior to crystallization, VAPOR ...Details: Hampton CSHT condition D12, 2.0 M ammonium phosphate, 0.1 M Tris pH 8.5, 26.5 mg/mL protein, crystal tracking ID 204803d12, expression tag not removed prior to crystallization, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. obs: 32905 / % possible obs: 96.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.46
Reflection shellResolution: 1.61→1.67 Å / Redundancy: 2 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 2.09 / Num. unique all: 2802 / % possible all: 84.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.23 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.7 Å
Translation2.5 Å30.7 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XHD

1xhd


Resolution: 1.61→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.181 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.872 / SU B: 2.803 / SU ML: 0.044 / SU R Cruickshank DPI: 0.072 / SU Rfree: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1674 5.1 %RANDOM
Rwork0.176 ---
obs0.176 32887 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.39 Å2 / Biso mean: 12.376 Å2 / Biso min: 5.42 Å2
Refinement stepCycle: LAST / Resolution: 1.61→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1227 0 1 195 1423
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221367
X-RAY DIFFRACTIONr_angle_refined_deg1.2011.9621876
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0785198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.04122.850
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.52815246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.9591510
X-RAY DIFFRACTIONr_chiral_restr0.080.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021016
X-RAY DIFFRACTIONr_mcbond_it0.4511.5872
X-RAY DIFFRACTIONr_mcangle_it0.85221419
X-RAY DIFFRACTIONr_scbond_it1.5233495
X-RAY DIFFRACTIONr_scangle_it2.5064.5441
LS refinement shellResolution: 1.61→1.652 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 81 -
Rwork0.338 1908 -
all-1989 -
obs--80.49 %
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)
12.1365-0.6611.95633.3790.02548.5329-0.03090.14450.1571-0.3224-0.0439-0.1609-0.5140.26530.07480.1066-0.0327-0.01290.03830.03040.034732.05647.96842.6064
20.78910.12390.17821.170.40081.8713-0.00580.03720.1151-0.0982-0.0220.0201-0.1764-0.00110.02770.04340.006-0.01080.0056-0.0020.034132.03975.474853.6075
31.4274-0.0467-0.46721.18690.17021.2286-0.00520.04630.0633-0.0647-0.04550.09870.015-0.13830.05070.02280.0042-0.01290.0367-0.02420.03523.0227-2.052961.4133
40.41690.17330.23562.18720.90022.7949-0.027-0.0697-0.0610.1524-0.03980.19670.2274-0.2390.06680.0416-0.03070.04380.0574-0.02520.069118.3018-7.80170.9023
54.8332.5257-3.9851.7608-2.7335.40560.1064-0.21060.01730.0747-0.1420.0044-0.14210.28350.03560.0295-0.00230.00970.045-0.03170.049929.18625.509775.2759
66.2482-1.9305-0.4975.82762.43421.13940.06180.05060.298-0.3353-0.0041-0.188-0.20650.0638-0.05770.0718-0.0295-0.00330.0476-0.01020.057140.311910.585963.9356
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 15
2X-RAY DIFFRACTION2A16 - 67
3X-RAY DIFFRACTION3A68 - 126
4X-RAY DIFFRACTION4A127 - 148
5X-RAY DIFFRACTION5A149 - 160
6X-RAY DIFFRACTION6A161 - 170

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