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- PDB-5d6a: 2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vib... -

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Basic information

Entry
Database: PDB / ID: 5d6a
Title2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in Complex with Adenylyl-imidodiphosphate (AMP-PNP)
ComponentsPredicted ATPase of the ABC class
KeywordsHYDROLASE / ABC transporter ATPase / AMP-PNP / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ABC transporter, ATPase, putative / ATPase of the ABC class, N-terminal / ATPase of the ABC class, C-terminal / : / P-loop domain / ATPase of the ABC class N-terminal / MRB1590 C-terminal domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Predicted ATPase of the ABC class
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 2.7 Angstrom Crystal Structure of ABC transporter ATPase from Vibrio vulnificus in Complex with Adenylyl-imidodiphosphate (AMP-PNP)
Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_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.value / _struct_conn.pdbx_dist_value / _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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted ATPase of the ABC class
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4453
Polymers64,9161
Non-polymers5292
Water1,51384
1
A: Predicted ATPase of the ABC class
hetero molecules

A: Predicted ATPase of the ABC class
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8906
Polymers129,8322
Non-polymers1,0584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area7820 Å2
ΔGint-65 kcal/mol
Surface area41990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.957, 104.957, 85.354
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-764-

HOH

21A-771-

HOH

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Components

#1: Protein Predicted ATPase of the ABC class


Mass: 64915.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: YJ016 / Gene: VVA0769 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q7MEA1
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsThe sequence has not yet been deposited to UniProt. See WP_011081233.1 database reference

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Protein: 5.9 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCL (pH 8.3), 1mM AMPPNP; Screen: PACT (C2), 0.1M PCB buffer (pH 5.0), 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2014
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 15243 / Num. obs: 15243 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 32.5
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
BLU-MAXdata collection
HKL-3000phasing
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→28.55 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.908 / SU B: 28.361 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25555 1535 10.1 %RANDOM
Rwork0.1941 ---
obs0.19991 13687 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.709 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 2.7→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4297 0 32 84 4413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0194433
X-RAY DIFFRACTIONr_bond_other_d0.0010.024210
X-RAY DIFFRACTIONr_angle_refined_deg1.0511.976006
X-RAY DIFFRACTIONr_angle_other_deg0.6739672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.7715550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.50124.46213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg7.76415722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.9351530
X-RAY DIFFRACTIONr_chiral_restr0.0620.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.025068
X-RAY DIFFRACTIONr_gen_planes_other0.0150.021033
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_it1.1563.472200
X-RAY DIFFRACTIONr_mcbond_other1.1553.4682199
X-RAY DIFFRACTIONr_mcangle_it2.0495.2032750
X-RAY DIFFRACTIONr_mcangle_other2.0495.2062751
X-RAY DIFFRACTIONr_scbond_it1.1473.5962233
X-RAY DIFFRACTIONr_scbond_other1.1473.5972234
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9285.3463257
X-RAY DIFFRACTIONr_long_range_B_refined4.12527.5635039
X-RAY DIFFRACTIONr_long_range_B_other4.08627.5475030
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.702→2.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 111 -
Rwork0.25 987 -
obs--99.64 %
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)
12.5783-1.5642-1.09564.20540.96792.79040.0148-0.0410.3827-0.09140.25290.4665-0.3949-0.2305-0.26770.1247-0.04570.00030.16860.08130.2233-46.140554.7025-5.0982
22.3798-1.4882-0.17783.71250.08890.89670.05980.32830.0838-0.2401-0.030.0949-0.17550.1254-0.02980.1472-0.140.04170.2004-0.03140.0342-31.848143.0456-11.2409
31.20550.3312-0.63791.3653-0.15292.4073-0.07090.034-0.36060.01930.0763-0.1990.10340.146-0.00540.0313-0.03470.03390.0837-0.06710.1844-26.20924.06535.2704
40.4514-0.63771.5330.91-2.10216.9826-0.0232-0.0841-0.07990.07030.13550.12-0.08140.0727-0.11220.2317-0.0048-0.00860.15190.00670.2154-14.20813.207322.2978
53.7237-1.1578-0.87682.52470.41711.8896-0.201-0.257-0.60230.04060.1777-0.29680.33460.2730.02330.09330.00020.01850.12510.00520.2271-25.199819.09987.8665
63.22460.79120.25424.4933-1.0843.4592-0.20830.032-0.2107-0.01510.17360.169-0.0019-0.2610.03470.0217-0.01950.02930.06-0.030.0507-42.312133.495210.8465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 125
2X-RAY DIFFRACTION2A126 - 216
3X-RAY DIFFRACTION3A217 - 340
4X-RAY DIFFRACTION4A341 - 360
5X-RAY DIFFRACTION5A361 - 462
6X-RAY DIFFRACTION6A463 - 551

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