2PYB - Header Asymmetric Unit

HEADER METAL TRANSPORT 16-MAY-07 2PYB

TITLE NAPA PROTEIN FROM BORRELIA BURGDORFERI

COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL ACTIVATING PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: NAPA; COMPND 5 ENGINEERED: YES

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BORRELIA BURGDORFERI; SOURCE 3 STRAIN: B31; SOURCE 4 GENE: NAPA; SOURCE 5 EXPRESSION_SYSTEM: BACILLUS SUBTILIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1423; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: SMS 118; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSM214G-NAPA

KEYWDS FERRITIN, DPS, FOUR-HELIX BUNDLE, METAL TRANSPORT

EXPDTA X-RAY DIFFRACTION

AUTHOR G.ZANOTTI,E.PAPINUTTO,M.DE BERNARD

REVDAT 4 26-OCT-16 2PYB 1 JRNL REVDAT 3 13-JUL-11 2PYB 1 VERSN REVDAT 2 24-FEB-09 2PYB 1 VERSN REVDAT 1 12-AUG-08 2PYB 0

JRNL AUTH G.CODOLO,E.PAPINUTTO,A.POLENGHI,M.M.D'ELIOS,G.ZANOTTI, JRNL AUTH 2 M.DE BERNARD JRNL TITL STRUCTURE AND IMMUNOMODULATORY PROPERTY RELATIONSHIP IN NAPA JRNL TITL 2 OF BORRELIA BURGDORFERI. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1804 2191 2010 JRNL REFN ISSN 0006-3002 JRNL PMID 20851780 JRNL DOI 10.1016/J.BBAPAP.2010.09.004

REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH G.ZANOTTI,E.PAPINUTTO,W.DUNDON,R.BATTISTUTTA,M.SEVESO, REMARK 1 AUTH 2 G.DAL GIUDICE,C.MONTECUCCO REMARK 1 TITL STRUCTURE OF THE NEUTROPHIL-ACTIVATING PROTEIN FROM REMARK 1 TITL 2 HELICOBACTER PYLORI REMARK 1 REF J.MOL.BIOL. V. 323 125 2002 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.A.GRANT,D.J.FILMAN,S.E.FINKEL,R.KOLTER,J.M.HOGLE REMARK 1 TITL THE CRYSTAL STRUCTURE OF DPS, A FERRITIN HOMOLOG THAT BINDS REMARK 1 TITL 2 AND PROTECTS DNA REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 5 294 1998 REMARK 1 REFN ISSN 1545-9993 REMARK 1 REFERENCE 3 REMARK 1 AUTH A.ILARI,S.STEFANINI,E.CHIANCONE,D.TSERNOGLOU REMARK 1 TITL THE DODECAMERIC FERRITIN FROM LISTERIA INNOCUA CONTAINS A REMARK 1 TITL 2 NOVEL INTERSUBUNIT IRON BINDING SITE REMARK 1 REF NAT.STRUCT.MOL.BIOL. V. 7 38 2000 REMARK 1 REFN ISSN 1545-9993

REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2005816.700 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 22533 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.242 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.400 REMARK 3 FREE R VALUE TEST SET COUNT : 1661 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3445 REMARK 3 BIN R VALUE (WORKING SET) : 0.3736 REMARK 3 BIN FREE R VALUE : 0.4512 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 272 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4984 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 24 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 52.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.34000 REMARK 3 B22 (A**2) : 0.34000 REMARK 3 B33 (A**2) : -0.67000 REMARK 3 B12 (A**2) : 4.89000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.54 REMARK 3 ESD FROM SIGMAA (A) : 0.74 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.63 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.99 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.300 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.260 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.960 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.680 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.460 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.34 REMARK 3 BSOL : 75.52 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER_REP.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE DATA IS MEROHEDRAL TWINNING WITH REMARK 3 TWINNING OPERATOR: (H,-H-K,-L) AND THE TWINNED FRACTION 0.45.

REMARK 4 REMARK 4 2PYB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-MAY-07. REMARK 100 THE RCSB ID CODE IS RCSB042918.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22533 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.38800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE AND 26-30% MPD, PH REMARK 280 4.5, VAPOR DIFFUSION, TEMPERATURE 293K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 X+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.53900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 26.86930 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.83333 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 46.53900 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 26.86930 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 75.83333 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 46.53900 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 26.86930 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 75.83333 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 53.73861 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 151.66667 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 53.73861 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 151.66667 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 53.73861 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 151.66667 REMARK 290 REMARK 290 REMARK: NULL

REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DODECAMER, GENERATE BY THE 3- REMARK 300 FOLD AXIS FROM THE TETRAMER CONTAINED IN THE ASYMMETRIC UNIT

REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DODECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DODECAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 47760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 70180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -467.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 93.07800 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 46.53900 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 80.60791 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000

REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH C 512 O HOH D 511 1.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ILE A 49 CB ILE A 49 CG1 0.204 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 49 CB - CG1 - CD1 ANGL. DEV. = 16.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASP A 12 174.99 -40.11 REMARK 500 ALA A 15 -99.95 -33.25 REMARK 500 ILE A 41 136.86 -24.99 REMARK 500 LYS A 42 82.24 -155.83 REMARK 500 PHE A 46 -91.21 24.31 REMARK 500 PHE A 47 -49.54 -26.54 REMARK 500 LEU A 74 -81.12 -70.71 REMARK 500 PHE A 80 1.15 -152.82 REMARK 500 PHE A 85 -53.40 -120.63 REMARK 500 MET A 86 31.39 -75.83 REMARK 500 LYS A 87 -47.03 -148.52 REMARK 500 ASP A 95 -165.72 -65.63 REMARK 500 ILE A 96 32.56 -89.77 REMARK 500 GLU A 97 -156.28 44.44 REMARK 500 SER A 98 -31.74 -147.35 REMARK 500 SER A 105 -83.27 -27.83 REMARK 500 SER A 108 -68.84 16.77 REMARK 500 SER A 112 -44.95 -143.29 REMARK 500 MET A 123 -76.16 -44.02 REMARK 500 ARG A 124 -46.37 -20.32 REMARK 500 ASP A 128 21.56 -77.81 REMARK 500 THR A 129 -61.55 -143.72 REMARK 500 ALA A 130 -5.49 -56.15 REMARK 500 ASP A 140 1.40 -68.97 REMARK 500 ASP A 145 -80.82 -44.25 REMARK 500 LYS A 154 13.72 -62.63 REMARK 500 LEU A 157 -81.74 -115.67 REMARK 500 ASN A 159 -118.49 -49.47 REMARK 500 CYS A 160 -140.18 94.04 REMARK 500 ASP B 12 174.75 -40.47 REMARK 500 LEU B 13 46.71 70.35 REMARK 500 ALA B 15 -99.56 -34.33 REMARK 500 ILE B 41 136.97 -25.32 REMARK 500 LYS B 42 83.18 -156.06 REMARK 500 PHE B 46 -90.91 24.36 REMARK 500 ILE B 49 -1.50 -59.84 REMARK 500 LEU B 74 -81.83 -70.04 REMARK 500 PHE B 80 1.26 -152.24 REMARK 500 PHE B 85 -53.53 -121.11 REMARK 500 MET B 86 32.53 -76.65 REMARK 500 LYS B 87 -47.08 -148.46 REMARK 500 ASP B 95 -165.58 -66.45 REMARK 500 ILE B 96 32.89 -89.80 REMARK 500 GLU B 97 -155.65 42.46 REMARK 500 SER B 98 -30.73 -147.48 REMARK 500 SER B 105 -81.74 -28.88 REMARK 500 SER B 108 -68.82 17.22 REMARK 500 SER B 112 -44.47 -144.29 REMARK 500 MET B 123 -75.38 -44.79 REMARK 500 ARG B 124 -47.03 -19.64 REMARK 500 REMARK 500 THIS ENTRY HAS 117 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 57 0.08 SIDE CHAIN REMARK 500 TYR B 57 0.07 SIDE CHAIN REMARK 500 TYR D 57 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 506 DISTANCE = 5.15 ANGSTROMS

REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE A 503 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 65 OD1 REMARK 620 2 ASP A 65 OD2 54.0 REMARK 620 3 GLU A 69 OE2 80.3 73.8 REMARK 620 4 HIS B 38 NE2 94.4 147.2 113.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 501 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 65 OD1 REMARK 620 2 ASP B 65 OD2 56.7 REMARK 620 3 GLU B 69 OE2 85.6 78.2 REMARK 620 4 HOH B 503 O 152.6 97.4 98.5 REMARK 620 5 HIS A 38 NE2 95.0 149.9 112.6 108.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE D 505 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 38 NE2 REMARK 620 2 ASP D 65 OD1 94.6 REMARK 620 3 ASP D 65 OD2 149.7 56.2 REMARK 620 4 GLU D 69 OE2 107.0 82.4 79.1 REMARK 620 5 HOH C 510 O 96.6 157.3 108.5 112.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 507 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 65 OD1 REMARK 620 2 ASP C 65 OD2 55.1 REMARK 620 3 GLU C 69 OE2 84.7 78.6 REMARK 620 4 HIS D 38 NE2 98.8 148.9 119.0 REMARK 620 5 HOH D 511 O 144.3 106.9 124.7 84.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 506 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 510 O REMARK 620 2 HOH C 511 O 63.9 REMARK 620 3 HIS C 50 NE2 125.4 170.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 508 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 512 O REMARK 620 2 HOH D 511 O 53.4 REMARK 620 N 1

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE D 505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE C 506 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE C 507 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE C 508

REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JI4 RELATED DB: PDB REMARK 900 NAP PROTEIN FROM HELICOBACTER PYLORI REMARK 900 RELATED ID: 1JI5 RELATED DB: PDB REMARK 900 DPL-1 FROM BACILLUS ANTHRACIS REMARK 900 RELATED ID: 1JIG RELATED DB: PDB REMARK 900 DLP-2 FROM BACILLUS ANTHRACIS REMARK 900 RELATED ID: 1DPS RELATED DB: PDB REMARK 900 DPS FROM E. COLI

DBREF 2PYB A 11 161 UNP O51633 O51633_BORBU 22 172 DBREF 2PYB B 11 161 UNP O51633 O51633_BORBU 22 172 DBREF 2PYB C 11 161 UNP O51633 O51633_BORBU 22 172 DBREF 2PYB D 11 161 UNP O51633 O51633_BORBU 22 172

SEQRES 1 A 151 ASP ASP LEU ASP ALA ILE GLN LEU LYS LEU GLN GLU LEU SEQRES 2 A 151 LEU ALA SER LEU HIS ILE PHE TYR SER ASN LEU ARG GLY SEQRES 3 A 151 ILE HIS TRP ASN ILE LYS ASP THR ASN PHE PHE VAL ILE SEQRES 4 A 151 HIS LYS LYS THR GLN LYS LEU TYR GLU TYR ILE GLU LYS SEQRES 5 A 151 ILE ILE ASP ILE VAL ALA GLU ARG SER ARG MET LEU GLY SEQRES 6 A 151 TYR ASP SER GLU PHE ARG TYR SER GLU PHE MET LYS LYS SEQRES 7 A 151 SER PHE ILE LYS GLU LEU ASP ILE GLU SER THR SER ASN SEQRES 8 A 151 PHE LEU PRO SER MET GLU SER ILE VAL CYS SER LEU THR SEQRES 9 A 151 GLU ILE LEU LYS ASN ILE PHE GLY MET ARG LYS LEU ILE SEQRES 10 A 151 ASP THR ALA GLY ASP TYR GLY THR ALA ASN ILE MET ASP SEQRES 11 A 151 ASP ILE MET SER ASP LEU GLU LYS HIS LEU TRP MET HIS SEQRES 12 A 151 LYS ALA LEU LEU GLU ASN CYS ASP SEQRES 1 B 151 ASP ASP LEU ASP ALA ILE GLN LEU LYS LEU GLN GLU LEU SEQRES 2 B 151 LEU ALA SER LEU HIS ILE PHE TYR SER ASN LEU ARG GLY SEQRES 3 B 151 ILE HIS TRP ASN ILE LYS ASP THR ASN PHE PHE VAL ILE SEQRES 4 B 151 HIS LYS LYS THR GLN LYS LEU TYR GLU TYR ILE GLU LYS SEQRES 5 B 151 ILE ILE ASP ILE VAL ALA GLU ARG SER ARG MET LEU GLY SEQRES 6 B 151 TYR ASP SER GLU PHE ARG TYR SER GLU PHE MET LYS LYS SEQRES 7 B 151 SER PHE ILE LYS GLU LEU ASP ILE GLU SER THR SER ASN SEQRES 8 B 151 PHE LEU PRO SER MET GLU SER ILE VAL CYS SER LEU THR SEQRES 9 B 151 GLU ILE LEU LYS ASN ILE PHE GLY MET ARG LYS LEU ILE SEQRES 10 B 151 ASP THR ALA GLY ASP TYR GLY THR ALA ASN ILE MET ASP SEQRES 11 B 151 ASP ILE MET SER ASP LEU GLU LYS HIS LEU TRP MET HIS SEQRES 12 B 151 LYS ALA LEU LEU GLU ASN CYS ASP SEQRES 1 C 151 ASP ASP LEU ASP ALA ILE GLN LEU LYS LEU GLN GLU LEU SEQRES 2 C 151 LEU ALA SER LEU HIS ILE PHE TYR SER ASN LEU ARG GLY SEQRES 3 C 151 ILE HIS TRP ASN ILE LYS ASP THR ASN PHE PHE VAL ILE SEQRES 4 C 151 HIS LYS LYS THR GLN LYS LEU TYR GLU TYR ILE GLU LYS SEQRES 5 C 151 ILE ILE ASP ILE VAL ALA GLU ARG SER ARG MET LEU GLY SEQRES 6 C 151 TYR ASP SER GLU PHE ARG TYR SER GLU PHE MET LYS LYS SEQRES 7 C 151 SER PHE ILE LYS GLU LEU ASP ILE GLU SER THR SER ASN SEQRES 8 C 151 PHE LEU PRO SER MET GLU SER ILE VAL CYS SER LEU THR SEQRES 9 C 151 GLU ILE LEU LYS ASN ILE PHE GLY MET ARG LYS LEU ILE SEQRES 10 C 151 ASP THR ALA GLY ASP TYR GLY THR ALA ASN ILE MET ASP SEQRES 11 C 151 ASP ILE MET SER ASP LEU GLU LYS HIS LEU TRP MET HIS SEQRES 12 C 151 LYS ALA LEU LEU GLU ASN CYS ASP SEQRES 1 D 151 ASP ASP LEU ASP ALA ILE GLN LEU LYS LEU GLN GLU LEU SEQRES 2 D 151 LEU ALA SER LEU HIS ILE PHE TYR SER ASN LEU ARG GLY SEQRES 3 D 151 ILE HIS TRP ASN ILE LYS ASP THR ASN PHE PHE VAL ILE SEQRES 4 D 151 HIS LYS LYS THR GLN LYS LEU TYR GLU TYR ILE GLU LYS SEQRES 5 D 151 ILE ILE ASP ILE VAL ALA GLU ARG SER ARG MET LEU GLY SEQRES 6 D 151 TYR ASP SER GLU PHE ARG TYR SER GLU PHE MET LYS LYS SEQRES 7 D 151 SER PHE ILE LYS GLU LEU ASP ILE GLU SER THR SER ASN SEQRES 8 D 151 PHE LEU PRO SER MET GLU SER ILE VAL CYS SER LEU THR SEQRES 9 D 151 GLU ILE LEU LYS ASN ILE PHE GLY MET ARG LYS LEU ILE SEQRES 10 D 151 ASP THR ALA GLY ASP TYR GLY THR ALA ASN ILE MET ASP SEQRES 11 D 151 ASP ILE MET SER ASP LEU GLU LYS HIS LEU TRP MET HIS SEQRES 12 D 151 LYS ALA LEU LEU GLU ASN CYS ASP

HET FE A 502 1 HET FE A 503 1 HET FE A 504 1 HET FE B 501 1 HET FE C 506 1 HET FE C 507 1 HET FE C 508 1 HET FE D 505 1

HETNAM FE FE (III) ION

FORMUL 5 FE 8(FE 3+) FORMUL 13 HOH *24(H2 O)

HELIX 1 1 ASP A 14 ILE A 41 1 28 HELIX 2 2 PHE A 46 GLU A 58 1 13 HELIX 3 3 ILE A 60 GLY A 75 1 16 HELIX 4 4 SER A 112 GLY A 131 1 20 HELIX 5 5 ASP A 132 LYS A 154 1 23 HELIX 6 6 ASP B 14 ILE B 41 1 28 HELIX 7 7 PHE B 46 GLU B 58 1 13 HELIX 8 8 GLU B 58 GLY B 75 1 18 HELIX 9 9 SER B 112 GLY B 131 1 20 HELIX 10 10 ASP B 132 LYS B 154 1 23 HELIX 11 11 ASP C 14 ILE C 41 1 28 HELIX 12 12 PHE C 46 GLU C 58 1 13 HELIX 13 13 ILE C 60 GLY C 75 1 16 HELIX 14 14 SER C 112 GLY C 131 1 20 HELIX 15 15 ASP C 132 LYS C 154 1 23 HELIX 16 16 ASP D 14 ILE D 41 1 28 HELIX 17 17 PHE D 46 LYS D 52 1 7 HELIX 18 18 THR D 53 GLU D 58 1 6 HELIX 19 19 GLU D 58 GLY D 75 1 18 HELIX 20 20 SER D 112 GLY D 131 1 20 HELIX 21 21 ASP D 132 LYS D 154 1 23

LINK OD1 ASP A 65 FE FE A 503 1555 1555 2.42 LINK OD2 ASP A 65 FE FE A 503 1555 1555 2.38 LINK OE2 GLU A 69 FE FE A 503 1555 1555 2.37 LINK NE2 HIS B 38 FE FE A 503 1555 1555 2.54 LINK OD1 ASP B 65 FE FE B 501 1555 1555 2.40 LINK OD2 ASP B 65 FE FE B 501 1555 1555 2.23 LINK OE2 GLU B 69 FE FE B 501 1555 1555 2.32 LINK NE2 HIS C 38 FE FE D 505 1555 1555 2.58 LINK OD1 ASP C 65 FE FE C 507 1555 1555 2.34 LINK OD2 ASP C 65 FE FE C 507 1555 1555 2.41 LINK OE2 GLU C 69 FE FE C 507 1555 1555 2.30 LINK NE2 HIS D 38 FE FE C 507 1555 1555 2.42 LINK OD1 ASP D 65 FE FE D 505 1555 1555 2.34 LINK OD2 ASP D 65 FE FE D 505 1555 1555 2.33 LINK OE2 GLU D 69 FE FE D 505 1555 1555 2.44 LINK FE FE B 501 O HOH B 503 1555 1555 2.27 LINK FE FE A 502 O HOH B 503 1555 1555 1.92 LINK FE FE A 504 O HOH B 502 1555 1555 1.80 LINK FE FE D 505 O HOH C 510 1555 1555 2.37 LINK FE FE C 506 O HOH C 510 1555 1555 2.38 LINK FE FE C 506 O HOH C 511 1555 1555 2.11 LINK FE FE C 507 O HOH D 511 1555 1555 2.28 LINK FE FE C 508 O HOH C 512 1555 1555 2.01 LINK FE FE C 508 O HOH D 511 1555 1555 2.31 LINK NE2 HIS A 38 FE FE B 501 1555 1555 2.63 LINK NE2 HIS C 50 FE FE C 506 1555 1555 2.71

SITE 1 AC1 4 HIS A 38 ASP B 65 GLU B 69 HOH B 503 SITE 1 AC2 3 HIS A 50 GLU B 69 HOH B 503 SITE 1 AC3 3 ASP A 65 GLU A 69 HIS B 38 SITE 1 AC4 3 GLU A 69 HIS B 50 HOH B 502 SITE 1 AC5 4 HIS C 38 HOH C 510 ASP D 65 GLU D 69 SITE 1 AC6 4 HIS C 50 HOH C 510 HOH C 511 GLU D 69 SITE 1 AC7 5 ASP C 65 GLU C 69 HOH C 512 HIS D 38 SITE 2 AC7 5 HOH D 511 SITE 1 AC8 4 GLU C 69 HOH C 512 HIS D 50 HOH D 511

CRYST1 93.078 93.078 227.500 90.00 90.00 120.00 H 3 36

ORIGX1 1.000000 0.000000 0.000000 0.00000

ORIGX2 0.000000 1.000000 0.000000 0.00000

ORIGX3 0.000000 0.000000 1.000000 0.00000

SCALE1 0.010744 0.006203 0.000000 0.00000

SCALE2 0.000000 0.012406 0.000000 0.00000

SCALE3 0.000000 0.000000 0.004396 0.00000