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- PDB-1kbw: CRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF ANIA FROM NEISSERIA GO... -

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Basic information

Entry
Database: PDB / ID: 1kbw
TitleCRYSTAL STRUCTURE OF THE SOLUBLE DOMAIN OF ANIA FROM NEISSERIA GONORRHOEAE
ComponentsMajor outer membrane protein PAN 1
KeywordsOXIDOREDUCTASE / ANIA
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / : / cell outer membrane / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBoulanger, M.J. / Murphy, M.E.P.
CitationJournal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria: a new class of copper-containing nitrite reductases.
Authors: Boulanger, M.J. / Murphy, M.E.
History
DepositionNov 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: 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_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.ptnr2_auth_asym_id / _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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE ACCORDING TO THE AUTHOR THE SEQUENCE DIFFERENCES EXIST BETWEEN HIS SEQUENCE AND THE ...SEQUENCE ACCORDING TO THE AUTHOR THE SEQUENCE DIFFERENCES EXIST BETWEEN HIS SEQUENCE AND THE SWISSPROT ENTRY Q02219. AUTHOR'S SEQUENCE IS IDENTICAL TO THE SEQUENCE OBTAINGED FROM THE GONOCOCCAL GENOME SEQUENCING PROJECT (A49208) SUPPORTED BY USPHS/NIH GRANT #AI38399, AND B.A.ROE, L.SONG, S.P.LIN, X.YUAN, S.CLIFTON, T.DUCEY, L.LEWIS AND D.W.DYER AT THE UNIVERSITY OF OKLAHOMA - ACGT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major outer membrane protein PAN 1
B: Major outer membrane protein PAN 1
C: Major outer membrane protein PAN 1
D: Major outer membrane protein PAN 1
E: Major outer membrane protein PAN 1
F: Major outer membrane protein PAN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,03918
Polymers211,2766
Non-polymers76312
Water20,6091144
1
A: Major outer membrane protein PAN 1
B: Major outer membrane protein PAN 1
C: Major outer membrane protein PAN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0209
Polymers105,6383
Non-polymers3816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10480 Å2
ΔGint-74 kcal/mol
Surface area28630 Å2
MethodPISA
2
D: Major outer membrane protein PAN 1
E: Major outer membrane protein PAN 1
F: Major outer membrane protein PAN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,0209
Polymers105,6383
Non-polymers3816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-72 kcal/mol
Surface area28470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.230, 99.550, 103.710
Angle α, β, γ (deg.)83.55, 73.70, 73.01
Int Tables number1
Space group name H-MP1
DetailsThe physiological molecule is the homotrimer

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Components

#1: Protein
Major outer membrane protein PAN 1 / ANIA


Mass: 35212.746 Da / Num. of mol.: 6 / Fragment: Residues 42-364, soluble domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: aniA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: Q02219
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1144 / 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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 1.7 M (NH4)2SO4, 0.2 M LiSO4 and 0.1 M CAPS, pH 10.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.7 Mammonium sulfate1reservoir
20.2 M1reservoirLiSO4
30.1 MCAPS1reservoirpH10.5
415 mg/mlprotein1drop
510 mMTris1droppH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: May 15, 1999 / Details: mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 95282 / Num. obs: 76914 / % possible obs: 80.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 6.96
Reflection shellResolution: 2.4→2.55 Å / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 2.5 / Num. unique all: 11789 / % possible all: 74
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 100 Å
Reflection shell
*PLUS
Highest resolution: 2.4 Å / % possible obs: 74 % / Num. unique obs: 11789 / Rmerge(I) obs: 0.223

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→50 Å / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh and Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.234 6251 -random
Rwork0.211 ---
obs0.211 76029 80.7 %-
all-95041 --
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13746 0 12 1144 14902
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d1.516
X-RAY DIFFRACTIONc_angle_d2.262
X-RAY DIFFRACTIONc_mcangle_it1.524
X-RAY DIFFRACTIONc_mcbond_it0.925
LS refinement shellResolution: 2.4→2.55 Å / Num. reflection Rfree: 778 / Num. reflection obs: 11789
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg2.262
X-RAY DIFFRACTIONc_mcbond_it0.925
LS refinement shell
*PLUS
Highest resolution: 2.4 Å

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