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- PDB-2etv: Crystal structure of a putative fe(iii) abc transporter (tm0189) ... -

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Basic information

Entry
Database: PDB / ID: 2etv
TitleCrystal structure of a putative fe(iii) abc transporter (tm0189) from thermotoga maritima msb8 at 1.70 A resolution
Componentsiron(III) ABC transporter, periplasmic iron-binding protein, putative
KeywordsMETAL BINDING PROTEIN / Periplasmic iron-binding protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PHOSPHATE ION / : / Iron(III) ABC transporter, periplasmic iron-binding protein, putative
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of IRON(III) ABC transporter, periplasmic iron-binding protein, putative (tm0189) from THERMOTOGA MARITIMA at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE (1) THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] ...SEQUENCE (1) THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHH] FOLLOWED BY RESIDUES 25-358 OF THE PREDICTED TM0189 GENE PRODUCT. IN ORDER TO REMOVE A PREDICTED TRANSMEMBRANE HELIX, THE FIRST 24 RESIDUES WERE NOT INCLUDED IN THE CONSTRUCT. (2) THE PROTEIN WAS REDUCTIVELY METHYLATED PRIOR TO CRYSTALLIZATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iron(III) ABC transporter, periplasmic iron-binding protein, putative
B: iron(III) ABC transporter, periplasmic iron-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,66225
Polymers79,2582
Non-polymers1,40423
Water14,016778
1
A: iron(III) ABC transporter, periplasmic iron-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,37713
Polymers39,6291
Non-polymers74812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: iron(III) ABC transporter, periplasmic iron-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,28512
Polymers39,6291
Non-polymers65611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: iron(III) ABC transporter, periplasmic iron-binding protein, putative
hetero molecules

A: iron(III) ABC transporter, periplasmic iron-binding protein, putative
hetero molecules

A: iron(III) ABC transporter, periplasmic iron-binding protein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,13039
Polymers118,8873
Non-polymers2,24336
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area9240 Å2
ΔGint-19 kcal/mol
Surface area42950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.820, 109.820, 122.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-4-

PO4

21A-4-

PO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: HIS / End label comp-ID: TRP / Refine code: 2 / Auth seq-ID: -1 - 358 / Label seq-ID: 11 - 346

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein iron(III) ABC transporter, periplasmic iron-binding protein, putative


Mass: 39628.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm0189 / Production host: Escherichia coli (E. coli) / References: GenBank: 4980685, UniProt: Q9WY32*PLUS

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Non-polymers , 5 types, 801 molecules

#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 778 / 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: 2.6 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop
Details: 0.2M (NH4)2HPO4, 20.0% PEG-3350, No Buffer pH 7.9, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97960, 0.95372
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 4, 2005 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.953721
ReflectionResolution: 1.7→30 Å / Num. obs: 92056 / % possible obs: 92.8 % / Redundancy: 5.65 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 6.78
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.7680.40.7251.51417781444780.4
1.76-1.8384.60.8941.854496515413
1.83-1.9188.60.8942.364520815518
1.91-2.0291.70.8943.275299518221
2.02-2.1493.90.8944.464719916245
2.14-2.3195.80.8945.745216317945
2.31-2.5496.90.8947.35068817439
2.54-2.9980.8949.165118917589
2.9-3.6698.90.89412.255305718287
3.66-3099.20.89417.35303018134

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.077 / SU ML: 0.071 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.097
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2) A NICKEL ION IS COORDINATED IN AN OCTAHEDRAL COMPLEX TO THE SIDECHAINS OF HIS-1, HIS-3 ON THE SAME CHAIN; HIS-2, HIS-4 ON A SYMMETRY- ...Details: 1) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2) A NICKEL ION IS COORDINATED IN AN OCTAHEDRAL COMPLEX TO THE SIDECHAINS OF HIS-1, HIS-3 ON THE SAME CHAIN; HIS-2, HIS-4 ON A SYMMETRY-RELATED CHAIN, AND TWO WATER MOLECULES. X-RAY FLUORESCENCE SUPPORTS THE ASSIGNMENT OF THE NICKEL ION. 3) A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4) LYSINES 304 APPEARS TO HAVE BEEN PROTECTED FROM REDUCTIVE METHYLATION AND WAS MODELED AS LYSINE IN BOTH CHAINS. ALL OTHER LYSINES HAVE BEEN MODELED AS MLY (N-DIMETHYL-LYSINE).
RfactorNum. reflection% reflectionSelection details
Rfree0.207 4608 5 %RANDOM
Rwork0.163 ---
all0.165 ---
obs0.16514 87413 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.72 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.04 Å20 Å2
2--0.07 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5411 0 84 778 6273
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225690
X-RAY DIFFRACTIONr_bond_other_d0.0020.023941
X-RAY DIFFRACTIONr_angle_refined_deg1.57127694
X-RAY DIFFRACTIONr_angle_other_deg1.07439599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7335677
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.39224260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94315.152985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4971534
X-RAY DIFFRACTIONr_chiral_restr0.1040.2863
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026153
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021124
X-RAY DIFFRACTIONr_nbd_refined0.2190.21217
X-RAY DIFFRACTIONr_nbd_other0.1960.24232
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22762
X-RAY DIFFRACTIONr_nbtor_other0.0840.22758
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2557
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.252
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3340.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2850.235
X-RAY DIFFRACTIONr_mcbond_it1.96633499
X-RAY DIFFRACTIONr_mcbond_other0.53731381
X-RAY DIFFRACTIONr_mcangle_it2.51555488
X-RAY DIFFRACTIONr_scbond_it4.64882524
X-RAY DIFFRACTIONr_scangle_it6.228112205
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1959TIGHT POSITIONAL0.080.05
2418MEDIUM POSITIONAL0.420.5
1959TIGHT THERMAL0.350.5
2418MEDIUM THERMAL1.042
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 333 -
Rwork0.264 6438 -
obs--99.65 %
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)
10.568-0.17360.49550.3244-0.26941.8307-0.0073-0.01150.03480.04210.0232-0.0535-0.0630.053-0.0159-0.09290.00930.0038-0.1459-0.0049-0.100426.294970.433121.9805
20.87230.4333-0.40170.6714-0.15781.49050.01810.0161-0.08660.0064-0.0112-0.09220.05790.0125-0.0069-0.1144-0.00220.0021-0.1211-0.0361-0.065117.0996108.606222.3148
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-6 - 3586 - 346
22BB-1 - 35811 - 346

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