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- PDB-4hbf: Crystal structure of PpcA V13A mutant -

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Basic information

Entry
Database: PDB / ID: 4hbf
TitleCrystal structure of PpcA V13A mutant
ComponentsPpcA
KeywordsELECTRON TRANSPORT
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
: / Cytochrome c7-like / Cytochrome c7 and related cytochrome c / Cytochrome c, class III / Cytochrome C3 / Cytochrome C3 / Multiheme cytochrome superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacter sulfurreducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPokkuluri, P.R. / Schiffer, M.
CitationJournal: To be Published
Title: V13 mutants of PpcA
Authors: Pokkuluri, P.R. / Schiffer, M.
History
DepositionSep 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Mar 10, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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_comp_id / _struct_conn.ptnr1_auth_seq_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_type.id / _struct_ref_seq_dif.details / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PpcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,2568
Polymers7,7201
Non-polymers2,5367
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PpcA
hetero molecules

A: PpcA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,51316
Polymers15,4402
Non-polymers5,07314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/41
Buried area11030 Å2
ΔGint-213 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.200, 32.200, 178.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein PpcA


Mass: 7720.096 Da / Num. of mol.: 1 / Fragment: PpcA / Mutation: V13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens (bacteria) / Gene: ppcA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GGK7
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-DXC / (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID / DEOXYCHOLIC ACID


Mass: 392.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40O4 / Comment: detergent*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3 Å3/Da / Density % sol: 59.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 3.7 M ammonium sulfate pH adjusted to 6.0 with ammonium hydroxide; 0.25% deoxycholate in the drop, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 1.0332 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Apr 13, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.9→90 Å / Num. obs: 7763 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 58.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.087 / Mean I/σ(I) obs: 16.1 / Num. unique all: 554 / % possible all: 73.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OS6

1os6


Resolution: 1.9→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.397 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22949 752 9.8 %RANDOM
Rwork0.18784 ---
obs0.192 6920 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.277 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms530 0 172 73 775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022742
X-RAY DIFFRACTIONr_bond_other_d0.0040.02579
X-RAY DIFFRACTIONr_angle_refined_deg1.4792.5521037
X-RAY DIFFRACTIONr_angle_other_deg0.91231365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.678570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.281
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02728
X-RAY DIFFRACTIONr_gen_planes_other0.0040.0288
X-RAY DIFFRACTIONr_nbd_refined0.390.2220
X-RAY DIFFRACTIONr_nbd_other0.30.2943
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.2323
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.264
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0230.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.210.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3390.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9691.5351
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8972553
X-RAY DIFFRACTIONr_scbond_it2.3753391
X-RAY DIFFRACTIONr_scangle_it3.6194.5484
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.263 25
Rwork0.187 359

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