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- PDB-3li2: Closed Conformation of HtsA Complexed with Staphyloferrin A -

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Basic information

Entry
Database: PDB / ID: 3li2
TitleClosed Conformation of HtsA Complexed with Staphyloferrin A
ComponentsFerrichrome ABC transporter lipoprotein
KeywordsTRANSPORT PROTEIN / siderophore / iron / receptor / lipoprotein / binding protein
Function / homology
Function and homology information


ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Chem-SF8 / ABC transporter substrate-binding protein / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsGrigg, J.C. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The Staphylococcus aureus siderophore receptor HtsA undergoes localized conformational changes to enclose staphyloferrin A in an arginine-rich binding pocket.
Authors: Grigg, J.C. / Cooper, J.D. / Cheung, J. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionJan 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_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: Ferrichrome ABC transporter lipoprotein
B: Ferrichrome ABC transporter lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,11211
Polymers66,7192
Non-polymers1,3939
Water3,963220
1
A: Ferrichrome ABC transporter lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2168
Polymers33,3591
Non-polymers8577
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferrichrome ABC transporter lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8963
Polymers33,3591
Non-polymers5362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.280, 148.600, 52.270
Angle α, β, γ (deg.)90.000, 117.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ferrichrome ABC transporter lipoprotein


Mass: 33359.391 Da / Num. of mol.: 2 / Fragment: UNP residues 38-327
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria)
Strain: Newman / Gene: htsA, NWMN_2078 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6QJ18, UniProt: A0A0H3K9U6*PLUS

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Non-polymers , 5 types, 229 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SF8 / (2R)-2-(2-{[(1R)-1-carboxy-4-{[(3S)-3,4-dicarboxy-3-hydroxybutanoyl]amino}butyl]amino}-2-oxoethyl)-2-hydroxybutanedioic acid / Staphyloferrin A


Mass: 480.377 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H24N2O14
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.05 M zinc acetate, 20 % PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 7, 2008
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.509
11L, -K, H20.491
ReflectionResolution: 2.2→74.3 Å / Num. all: 35659 / Num. obs: 35659 / % possible obs: 99.2 % / Redundancy: 4 % / Rsym value: 0.085 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.309 / % possible all: 99.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
MOLREPphasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→33.15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 11.226 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE FRIEDEL PAIRS WERE USED FOR phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1776 5 %RANDOM
Rwork0.165 ---
obs0.168 35626 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 84.47 Å2 / Biso mean: 37.119 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1-8.23 Å20 Å2-10.46 Å2
2---6.61 Å20 Å2
3----1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.2→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4569 0 76 220 4865
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224791
X-RAY DIFFRACTIONr_angle_refined_deg1.4782.0016447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7565593
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.02625.369203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.05715969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.81525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213499
X-RAY DIFFRACTIONr_mcbond_it0.4731.52932
X-RAY DIFFRACTIONr_mcangle_it0.80624737
X-RAY DIFFRACTIONr_scbond_it1.44931859
X-RAY DIFFRACTIONr_scangle_it2.2294.51710
LS refinement shellResolution: 2.2→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 134 -
Rwork0.14 2446 -
all-2580 -
obs--97.58 %
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)
13.29382.03490.28084.36940.12312.45980.1696-0.1521-0.56740.4927-0.1244-0.02810.5687-0.0705-0.04520.2648-0.0192-0.02150.034-0.00360.202-6.5127-27.94722.9764
24.9565-0.6605-2.8425.5127-1.39912.5867-0.01460.85970.4358-1.03530.29090.0720.0719-0.3925-0.27630.3702-0.1548-0.11250.2926-0.00450.2115-6.1763-15.5809-8.533
33.28171.69670.56394.73180.29372.37930.10340.02-0.19190.3599-0.07830.20820.2047-0.0348-0.02520.1756-0.0281-0.00520.0005-0.01820.0838-6.0512-21.97034.0002
41.04850.6949-1.144611.4261.68811.9343-0.21310.4195-0.5338-0.44470.1203-1.06550.02590.06670.09290.2712-0.07080.10730.5936-0.2640.550118.4138-15.8547-6.7205
53.51512.04660.0575.0851.40733.8120.01140.0028-0.1630.13560.0491-0.377-0.34980.2315-0.06050.1557-0.0861-0.07550.11030.03860.125311.3036-4.64446.3161
64.2382-1.3167-2.7714.66614.62445.4798-0.1749-0.2995-0.31691.03530.1522-0.31560.73910.46630.02270.3697-0.1256-0.12710.15870.04420.309512.7114-6.538312.2453
71.17341.79990.74372.56721.30234.31520.1183-0.05060.10810.2238-0.0849-0.0767-0.14390.1545-0.03340.1861-0.018-0.07950.05440.02570.21359.17921.35248.5916
815.63785.04412.43061.13353.240610.7606-0.06010.08551.41470.1252-0.00560.5657-0.6061-0.20370.06570.5064-0.02080.04180.16670.20920.74096.631511.58891.4784
92.23952.0105-0.43815.8171-0.61671.3682-0.13770.4659-0.0108-0.22730.228-0.2302-0.37780.378-0.09020.2065-0.13860.030.2232-0.01820.091910.7924-0.7553-0.552
106.73095.22-5.405822.2332-3.85852.0849-0.46781.0565-0.1064-0.80750.5149-0.04480.0568-0.4143-0.04710.5451-0.53590.11550.7224-0.15520.168614.2575-8.0052-8.7851
114.08510.07282.15716.71790.49332.2704-0.24610.07930.5938-0.1929-0.09350.6276-0.6763-0.15450.33970.37670.0531-0.06450.0924-0.01330.21386.8308-29.092428.1938
121.4131-0.9016-1.60044.35141.55374.2958-0.0164-0.3944-0.30230.710.0495-0.64750.29510.7372-0.03310.28040.0171-0.13270.16740.07140.254717.3993-43.73532.0274
136.0893-1.5286-2.06571.39122.46613.3919-0.3643-1.0664-0.2740.67350.09840.28860.70510.06930.26590.6119-0.00780.21390.16740.01790.22464.3353-41.492835.7714
140.3533-1.764-0.15915.81341.81085.5734-0.04630.1876-0.0074-0.0961-0.27980.7775-0.4423-0.57570.32610.20630.0343-0.06330.08510.0780.41754.9696-38.767923.1326
152.3613-0.7950.03533.0432.21312.850.21320.23380.4077-0.75370.1444-0.9513-0.55350.4418-0.35770.3863-0.07150.16870.239-0.00440.392724.6801-40.881512.4886
164.739-0.92290.53956.21911.8674.08590.01430.0094-0.2828-0.34460.08990.45550.0374-0.3026-0.10420.21430.0128-0.02910.0920.01550.065311.656-55.163212.8174
178.5283-0.96224.45111.02862.0776.40760.34951.0580.323-0.4297-0.4030.2254-0.2033-0.05360.05350.37620.0848-0.17810.12840.01610.40528.1478-53.95717.8584
181.7491-0.78192.0076.21920.37811.9247-0.1304-0.0059-0.2766-0.28670.19570.3685-0.04550.0805-0.06530.23670.04550.03370.073-0.03010.175810.7992-61.737310.5322
191.3679-0.92560.33496.68231.8512.68240.20780.1281-0.38970.56580.118-0.14880.74210.1914-0.32580.27770.0274-0.08990.1411-0.05160.187717.8607-66.491814.3259
202.9786-0.7597-0.89551.36121.29887.6716-0.0286-0.2302-0.057-0.23320.4369-0.67430.50321.2476-0.40830.2188-0.02290.11760.2662-0.15460.395228.0667-52.919914.6814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 68
2X-RAY DIFFRACTION2A69 - 98
3X-RAY DIFFRACTION3A99 - 173
4X-RAY DIFFRACTION4A174 - 191
5X-RAY DIFFRACTION5A192 - 219
6X-RAY DIFFRACTION6A220 - 239
7X-RAY DIFFRACTION7A240 - 267
8X-RAY DIFFRACTION8A268 - 283
9X-RAY DIFFRACTION9A284 - 310
10X-RAY DIFFRACTION10A311 - 323
11X-RAY DIFFRACTION11B36 - 61
12X-RAY DIFFRACTION12B62 - 101
13X-RAY DIFFRACTION13B102 - 122
14X-RAY DIFFRACTION14B123 - 161
15X-RAY DIFFRACTION15B162 - 196
16X-RAY DIFFRACTION16B197 - 219
17X-RAY DIFFRACTION17B220 - 240
18X-RAY DIFFRACTION18B241 - 266
19X-RAY DIFFRACTION19B267 - 305
20X-RAY DIFFRACTION20B306 - 327

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