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- PDB-1vr5: Crystal structure of Oligopeptide ABC transporter, periplasmic ol... -

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Basic information

Entry
Database: PDB / ID: 1vr5
TitleCrystal structure of Oligopeptide ABC transporter, periplasmic oligopeptide-binding (TM1223) from THERMOTOGA MARITIMA at 1.73 A resolution
Componentsoligopeptide ABC transporter, periplasmic oligopeptide-binding protein
KeywordsPROTEIN TRANSPORT / TM1223 / OLIGOPEPTIDE ABC TRANSPORTER / PERIPLASMIC OLIGOPEPTIDE-BINDING / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


peptide transport / peptide transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Dipeptide-binding Protein; domain 1 / Dipeptide-binding Protein; Domain 1 / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.73 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Oligopeptide ABC transporter, periplasmic oligopeptide-binding (TM1223) from THERMOTOGA MARITIMA at 1.73 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / 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 / _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.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_type.id / _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 THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHHM] FOLLOWED ...SEQUENCE THE CONSTRUCT EXPRESSED COMPRISED AN N-TERMINAL PURIFICATION TAG [MGSDKIHHHHHHM] FOLLOWED BY RESIDUES 23-557 OF THE PREDICTED TM1223 GENE PRODUCT. IN ORDER TO REMOVE A PREDICTED TRANSMEMBRANE HELIX, THE FIRST 22 RESIDUES WERE NOT INCLUDED IN THE CONSTRUCT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
B: oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,75243
Polymers127,2072
Non-polymers2,54541
Water19,7801098
1
A: oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,16225
Polymers63,6031
Non-polymers1,55924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: oligopeptide ABC transporter, periplasmic oligopeptide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,59018
Polymers63,6031
Non-polymers98617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)140.030, 96.640, 115.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-583-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg label comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISLYSAA0 - 25712 - 247
21HISLYSBB0 - 25712 - 247
32LYSVALAA258 - 263248 - 253
42LYSVALBB258 - 263248 - 253
53THRALAAA264 - 556254 - 546
63THRALABB264 - 556254 - 546

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein oligopeptide ABC transporter, periplasmic oligopeptide-binding protein


Mass: 63603.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: TM1223 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0V0

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Non-polymers , 7 types, 1139 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1098 / 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: 2.79 Å3/Da / Density % sol: 55.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7
Details: 1.0M LiCl, 10.0% PEG-6000, 0.1M HEPES pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97933, 1.00003,0.97951
DetectorType: ADSC / Detector: CCD / Date: Jan 22, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979331
21.000031
30.979511
ReflectionResolution: 1.73→28.61 Å / Num. obs: 163581 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 32.24 Å2 / Rsym value: 0.087 / Net I/σ(I): 10.3
Reflection shellResolution: 1.73→1.82 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 23624 / Rsym value: 0.627 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
SCALA5.0)data scaling
SHELXDphasing
SHARPphasing
REFMAC5.2.0005refinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.73→28.61 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 4.071 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THERE ARE LOTS OF NON-WATER DENSITY IN THE SOLVENT REGION. THEY ARE MODELLED AS BUFFER OR CRYO PROTECTANT MOLECULES. HOWEVER, FOR MANY ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THERE ARE LOTS OF NON-WATER DENSITY IN THE SOLVENT REGION. THEY ARE MODELLED AS BUFFER OR CRYO PROTECTANT MOLECULES. HOWEVER, FOR MANY OF MOLECULES, THE DENSITIES ARE NOT WELL DEFINED. 3. RESIDUES ASP 362, ASP 366 AND GLU 370 MIGHT BE INVOLVED IN METAL BINDING. A SODIUM WAS TENATIVELY MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.18161 8214 5 %RANDOM
Rwork0.15164 ---
obs0.15314 155289 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.051 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å20 Å2
2--0.6 Å20 Å2
3----2.23 Å2
Refinement stepCycle: LAST / Resolution: 1.73→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8692 0 161 1098 9951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0229190
X-RAY DIFFRACTIONr_bond_other_d0.0020.028125
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.95112505
X-RAY DIFFRACTIONr_angle_other_deg0.879318927
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08251070
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6824.601426
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.412151415
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8471530
X-RAY DIFFRACTIONr_chiral_restr0.1020.21292
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021880
X-RAY DIFFRACTIONr_nbd_refined0.2220.21697
X-RAY DIFFRACTIONr_nbd_other0.1810.28182
X-RAY DIFFRACTIONr_nbtor_other0.0870.24800
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2781
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.225
X-RAY DIFFRACTIONr_mcbond_it1.96335398
X-RAY DIFFRACTIONr_mcbond_other0.60132146
X-RAY DIFFRACTIONr_mcangle_it3.08358768
X-RAY DIFFRACTIONr_scbond_it5.0384085
X-RAY DIFFRACTIONr_scangle_it7.121113737
X-RAY DIFFRACTIONr_nbtor_refined0.1930.24533
X-RAY DIFFRACTIONr_metal_ion_refined0.3240.28
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 8045 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.265
loose thermal1.710
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 646 5.41 %
Rwork0.239 11300 -
obs--99.92 %
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)
10.41010.2831-0.04780.78730.06470.44240.0053-0.0004-0.01170.11140.0238-0.00640.0013-0.0027-0.0291-0.0938-0.00330.0122-0.05730.0099-0.029589.991223.1395155.6984
20.5210.0936-0.18040.4872-0.04661.1089-0.0043-0.04310.0092-0.00290.0004-0.0145-0.0406-0.16940.0039-0.0614-0.0272-0.0002-0.06590.0004-0.023893.121919.90796.353
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 0 - 557 / Label seq-ID: 12 - 547

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB

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