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Basic information

Entry
Database: PDB / ID: 2yjp
TitleCrystal structure of the solute receptors for L-cysteine of Neisseria gonorrhoeae
ComponentsPUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
KeywordsTRANSPORT PROTEIN / SOLUTE-BINDING PROTEIN
Function / homology
Function and homology information


amino acid transport / outer membrane-bounded periplasmic space / extracellular region / metal ion binding
Similarity search - Function
: / Solute-binding protein family 3, conserved site / Bacterial extracellular solute-binding proteins, family 3 signature. / Bacterial periplasmic substrate-binding proteins / Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Prokaryotic membrane lipoprotein lipid attachment site profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CYSTEINE / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesNEISSERIA GONORRHOEAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsBulut, H. / Moniot, S. / Scheffel, F. / Gathmann, S. / Licht, A. / Saenger, W. / Schneider, E.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Crystal Structures of Two Solute Receptors for L-Cystine and L-Cysteine, Respectively, of the Human Pathogen Neisseria Gonorrhoeae.
Authors: Bulut, H. / Moniot, S. / Licht, A. / Scheffel, F. / Gathmann, S. / Saenger, W. / Schneider, E.
History
DepositionMay 23, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / 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 / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_symmetry / _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.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_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

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
B: PUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
C: PUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,46920
Polymers94,2103
Non-polymers1,25917
Water6,413356
1
A: PUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,10311
Polymers31,4031
Non-polymers70010
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6494
Polymers31,4031
Non-polymers2453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7175
Polymers31,4031
Non-polymers3144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.710, 91.590, 158.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A25 - 30
2113B25 - 30
3113C25 - 30
1213A32 - 82
2213B32 - 82
3213C32 - 82
1313A84 - 139
2313B84 - 139
3313C84 - 139
1413A144 - 160
2413B144 - 160
3413C144 - 160
1513A164 - 169
2513B164 - 169
3513C164 - 169
1613A182 - 199
2613B182 - 199
3613C182 - 199
1713A201 - 210
2713B201 - 210
3713C201 - 210
1813A215 - 229
2813B215 - 229
3813C215 - 229
1913A231 - 249
2913B231 - 249
3913C231 - 249
11013A251 - 268
21013B251 - 268
31013C251 - 268

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Components

#1: Protein PUTATIVE ABC TRANSPORTER, PERIPLASMIC BINDING PROTEIN, AMINO ACID / SOLUTE RECEPTORS FOR L-CYSTEINE


Mass: 31403.377 Da / Num. of mol.: 3 / Fragment: RESIDUES 18-284 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA GONORRHOEAE (bacteria) / Strain: FA 1090 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR PLYSS / References: UniProt: Q5F5B5
#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 23 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 23 TO ALA ...ENGINEERED RESIDUE IN CHAIN A, CYS 23 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 23 TO ALA ENGINEERED RESIDUE IN CHAIN C, CYS 23 TO ALA
Sequence detailsN-TERMINAL HIS-TAG CONSTRUCT WITH ENTEROKINASE CLEAVAGE SITE.

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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: 2.5 Å3/Da / Density % sol: 50.5 % / Description: NONE
Crystal growDetails: 16-18% PEG 4000, 100 MM HEPES PH 7.0, 10 MM ZNCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9395
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 2.26→47.18 Å / Num. obs: 39913 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.14 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.32
Reflection shellResolution: 2.26→2.38 Å / Redundancy: 2.92 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.25 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XT8

1xt8


Resolution: 2.26→47.18 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23274 1996 5 %RANDOM
Rwork0.18472 ---
obs0.18713 37917 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.081 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.26→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5620 0 53 356 6029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0225813
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.9727881
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4435744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46525.645248
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.37515972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4971521
X-RAY DIFFRACTIONr_chiral_restr0.120.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214399
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_it0.6931.53718
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.23625952
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4832095
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0534.51929
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A848tight positional0.090.05
2B848tight positional0.060.05
3C848tight positional0.10.05
1A733loose positional0.225
2B733loose positional0.185
3C733loose positional0.235
1A848tight thermal0.210.5
2B848tight thermal0.190.5
3C848tight thermal0.20.5
1A733loose thermal0.2310
2B733loose thermal0.2310
3C733loose thermal0.2310
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 122 -
Rwork0.224 2317 -
obs--100 %
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)
12.1918-0.04050.1551.58380.36362.84950.02260.2121-0.003-0.1947-0.071-0.0069-0.1920.05270.04830.05850.01550.01110.07640.00540.09147.5297.63422.897
21.6326-0.6378-0.08192.6337-0.2742.0088-0.0104-0.15260.15830.13140.0128-0.0448-0.11310.0774-0.00230.0126-0.0095-0.00490.0599-0.00890.055213.019.69946.679
32.2741-0.80711.21062.032-0.31752.20220.15-0.0711-0.4508-0.04310.00930.27540.2937-0.2414-0.15940.0631-0.0042-0.00540.1247-0.02760.14431.714-1.77727.051
41.8311-0.9886-0.09382.55750.54851.00440.08450.1004-0.2587-0.0766-0.05950.06840.17130.0112-0.02490.0602-0.0066-0.02590.12090.00270.084831.28720.32220.033
52.8199-0.51710.35892.2421-0.30371.65650.0767-0.1954-0.07630.072-0.00520.0720.07090.0099-0.07140.02020.00040.01280.05950.00020.027926.07333.14229.808
63.7842-1.90380.06242.26570.09281.41690.27990.49250.2571-0.4317-0.2386-0.2145-0.13180.0907-0.04130.10880.0170.01520.19710.00120.088338.16924.17311.433
71.45130.4552-0.6622.4855-1.24671.5130.07170.13920.1678-0.1755-0.00330.0166-0.01960.0454-0.06840.04110.0172-0.00050.111-0.00460.052512.19964.357.845
82.4151-0.5263-0.85312.64190.02033.13780.08050.1924-0.1089-0.2263-0.07690.03350.0863-0.0782-0.00370.02680.0008-0.01150.03810.00420.01596.7349.14912.637
93.00370.234-1.88621.8733-0.22352.09350.1529-0.39370.29690.3165-0.0757-0.0837-0.11010.5278-0.07730.0799-0.0324-0.01690.1728-0.01240.095219.01969.12416.014
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 122
2X-RAY DIFFRACTION2A123 - 215
3X-RAY DIFFRACTION3A216 - 350
4X-RAY DIFFRACTION4B24 - 143
5X-RAY DIFFRACTION5B144 - 215
6X-RAY DIFFRACTION6B216 - 350
7X-RAY DIFFRACTION7C24 - 143
8X-RAY DIFFRACTION8C144 - 215
9X-RAY DIFFRACTION9C216 - 350

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