PDB Short entry for 1X89 HEADER ANTIMICROBIAL PROTEIN 17-AUG-04 1X89 TITLE CRYSTAL STRUCTURE OF SIDEROCALIN (NGAL, LIPOCALIN 2) COMPLEXED WITH TITLE 2 CARBOXYMYCOBACTIN S COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: SIDEROCALIN, NGAL, P25, 25 KDA ALPHA-2-MICROGLOBULIN-RELATED COMPND 5 SUBUNIT OF MMP-9, LIPOCALIN 2, ONCOGENE 24P3; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: LCN2, NGAL, HNL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-DE3-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-3 KEYWDS LIPOCALIN, SIDEROPHORE, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.A.HOLMES,W.PAULSENE,X.JIDE,C.RATLEDGE,R.K.STRONG REVDAT 5 03-APR-24 1X89 1 REMARK REVDAT 4 20-OCT-21 1X89 1 REMARK SEQADV REVDAT 3 11-OCT-17 1X89 1 REMARK REVDAT 2 24-FEB-09 1X89 1 VERSN REVDAT 1 25-JAN-05 1X89 0 JRNL AUTH M.A.HOLMES,W.PAULSENE,X.JIDE,C.RATLEDGE,R.K.STRONG JRNL TITL SIDEROCALIN (LCN 2) ALSO BINDS CARBOXYMYCOBACTINS, JRNL TITL 2 POTENTIALLY DEFENDING AGAINST MYCOBACTERIAL INFECTIONS JRNL TITL 3 THROUGH IRON SEQUESTRATION JRNL REF STRUCTURE V. 13 29 2005 JRNL REFN ISSN 0969-2126 JRNL PMID 15642259 JRNL DOI 10.1016/J.STR.2004.10.009 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 46438 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : USED SAME SET AS PREVIOUSLY REMARK 3 -DETERMINED STRUCTURE REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 4270 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE : 0.2790 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 400 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4151 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 162 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.027 REMARK 3 BOND ANGLES (DEGREES) : 2.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1X89 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000030063. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-03 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 : ALS REMARK 200 BEAMLINE : 5.0.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46500 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.34500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: USED PREVIOUSLY-DETERMINED REMARK 200 STRUCTURE REMARK 200 SOFTWARE USED: USED PREVIOUSLY-DETERMINED STRUCTURE REMARK 200 STARTING MODEL: PREVIOUSLY-DETERMINED STRUCTURE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, SODIUM CHLORIDE, REMARK 280 ACETATE, PH 4.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.65000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 57.10000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 57.10000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.82500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 57.10000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 57.10000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 89.47500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 57.10000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.10000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.82500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 57.10000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.10000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 89.47500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 59.65000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 MONOMER. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C 221 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLN A 1 REMARK 465 ASP A 2 REMARK 465 SER A 3 REMARK 465 GLY A 178 REMARK 465 GLN B 1 REMARK 465 ASP B 2 REMARK 465 SER B 3 REMARK 465 ASP B 45 REMARK 465 LYS B 46 REMARK 465 ASP B 47 REMARK 465 GLY B 178 REMARK 465 GLN C 1 REMARK 465 ASP C 2 REMARK 465 SER C 3 REMARK 465 THR C 4 REMARK 465 GLY C 178 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 ASN A 96 CG OD1 ND2 REMARK 470 LYS A 98 CB CG CD CE NZ REMARK 470 ALA B 40 CB REMARK 470 ARG B 43 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 GLN B 49 CB CG CD OE1 NE2 REMARK 470 GLU B 60 CB CG CD OE1 OE2 REMARK 470 ASP B 61 CG OD1 OD2 REMARK 470 LYS B 62 CG CD CE NZ REMARK 470 ARG B 72 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 GLU B 143 CG CD OE1 OE2 REMARK 470 GLU B 150 CB CG CD OE1 OE2 REMARK 470 ASN B 151 CG OD1 ND2 REMARK 470 ARG B 154 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 163 CG CD OE1 OE2 REMARK 470 ASP C 45 CB CG OD1 OD2 REMARK 470 LYS C 46 CB CG CD CE NZ REMARK 470 ASP C 47 CB CG OD1 OD2 REMARK 470 GLU C 163 CG CD OE1 OE2 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 TYR A 56 CZ TYR A 56 CE2 0.079 REMARK 500 VAL C 16 CB VAL C 16 CG2 0.127 REMARK 500 VAL C 111 CB VAL C 111 CG2 0.131 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 LEU A 70 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 ASP A 77 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 PRO A 101 C - N - CA ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG A 109 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 140 CD - NE - CZ ANGL. DEV. = 11.2 DEGREES REMARK 500 ARG A 140 NE - CZ - NH1 ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 140 NE - CZ - NH2 ANGL. DEV. = -7.3 DEGREES REMARK 500 ARG B 140 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 PRO B 162 C - N - CA ANGL. DEV. = 9.5 DEGREES REMARK 500 VAL C 34 CG1 - CB - CG2 ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG C 81 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG C 140 CB - CG - CD ANGL. DEV. = 15.7 DEGREES REMARK 500 ARG C 140 CD - NE - CZ ANGL. DEV. = 13.4 DEGREES REMARK 500 ARG C 140 NE - CZ - NH1 ANGL. DEV. = 10.5 DEGREES REMARK 500 ARG C 140 NE - CZ - NH2 ANGL. DEV. = -8.9 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 47 77.12 -110.20 REMARK 500 TYR A 115 -36.41 68.47 REMARK 500 GLN A 117 -35.16 -144.23 REMARK 500 CYS A 175 -37.18 63.90 REMARK 500 LYS B 62 -3.71 82.49 REMARK 500 LYS B 74 15.54 58.42 REMARK 500 TYR B 115 -33.09 60.55 REMARK 500 GLN B 117 -52.78 -131.25 REMARK 500 CYS B 175 -40.05 64.07 REMARK 500 ASP C 47 48.35 76.28 REMARK 500 LYS C 62 -0.25 82.33 REMARK 500 TYR C 115 -42.45 63.94 REMARK 500 GLN C 117 -47.86 -131.37 REMARK 500 ASN C 129 17.65 50.45 REMARK 500 CYS C 175 -34.41 65.01 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 C 138 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CM1 A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CM1 B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CM1 C 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X71 RELATED DB: PDB REMARK 900 SIDEROCALIN COMPLEXED WITH TRENCAM-3,2-HOPO, A CEPABACTIN ANALOG REMARK 900 RELATED ID: 1X8U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SIDEROCALIN COMPLEXED WITH CARBOXYMYCOBACTIN T DBREF 1X89 A 1 178 UNP P80188 NGAL_HUMAN 21 198 DBREF 1X89 B 1 178 UNP P80188 NGAL_HUMAN 21 198 DBREF 1X89 C 1 178 UNP P80188 NGAL_HUMAN 21 198 SEQADV 1X89 SER A 87 UNP P80188 CYS 107 ENGINEERED MUTATION SEQADV 1X89 SER B 87 UNP P80188 CYS 107 ENGINEERED MUTATION SEQADV 1X89 SER C 87 UNP P80188 CYS 107 ENGINEERED MUTATION SEQRES 1 A 178 GLN ASP SER THR SER ASP LEU ILE PRO ALA PRO PRO LEU SEQRES 2 A 178 SER LYS VAL PRO LEU GLN GLN ASN PHE GLN ASP ASN GLN SEQRES 3 A 178 PHE GLN GLY LYS TRP TYR VAL VAL GLY LEU ALA GLY ASN SEQRES 4 A 178 ALA ILE LEU ARG GLU ASP LYS ASP PRO GLN LYS MET TYR SEQRES 5 A 178 ALA THR ILE TYR GLU LEU LYS GLU ASP LYS SER TYR ASN SEQRES 6 A 178 VAL THR SER VAL LEU PHE ARG LYS LYS LYS CYS ASP TYR SEQRES 7 A 178 TRP ILE ARG THR PHE VAL PRO GLY SER GLN PRO GLY GLU SEQRES 8 A 178 PHE THR LEU GLY ASN ILE LYS SER TYR PRO GLY LEU THR SEQRES 9 A 178 SER TYR LEU VAL ARG VAL VAL SER THR ASN TYR ASN GLN SEQRES 10 A 178 HIS ALA MET VAL PHE PHE LYS LYS VAL SER GLN ASN ARG SEQRES 11 A 178 GLU TYR PHE LYS ILE THR LEU TYR GLY ARG THR LYS GLU SEQRES 12 A 178 LEU THR SER GLU LEU LYS GLU ASN PHE ILE ARG PHE SER SEQRES 13 A 178 LYS SER LEU GLY LEU PRO GLU ASN HIS ILE VAL PHE PRO SEQRES 14 A 178 VAL PRO ILE ASP GLN CYS ILE ASP GLY SEQRES 1 B 178 GLN ASP SER THR SER ASP LEU ILE PRO ALA PRO PRO LEU SEQRES 2 B 178 SER LYS VAL PRO LEU GLN GLN ASN PHE GLN ASP ASN GLN SEQRES 3 B 178 PHE GLN GLY LYS TRP TYR VAL VAL GLY LEU ALA GLY ASN SEQRES 4 B 178 ALA ILE LEU ARG GLU ASP LYS ASP PRO GLN LYS MET TYR SEQRES 5 B 178 ALA THR ILE TYR GLU LEU LYS GLU ASP LYS SER TYR ASN SEQRES 6 B 178 VAL THR SER VAL LEU PHE ARG LYS LYS LYS CYS ASP TYR SEQRES 7 B 178 TRP ILE ARG THR PHE VAL PRO GLY SER GLN PRO GLY GLU SEQRES 8 B 178 PHE THR LEU GLY ASN ILE LYS SER TYR PRO GLY LEU THR SEQRES 9 B 178 SER TYR LEU VAL ARG VAL VAL SER THR ASN TYR ASN GLN SEQRES 10 B 178 HIS ALA MET VAL PHE PHE LYS LYS VAL SER GLN ASN ARG SEQRES 11 B 178 GLU TYR PHE LYS ILE THR LEU TYR GLY ARG THR LYS GLU SEQRES 12 B 178 LEU THR SER GLU LEU LYS GLU ASN PHE ILE ARG PHE SER SEQRES 13 B 178 LYS SER LEU GLY LEU PRO GLU ASN HIS ILE VAL PHE PRO SEQRES 14 B 178 VAL PRO ILE ASP GLN CYS ILE ASP GLY SEQRES 1 C 178 GLN ASP SER THR SER ASP LEU ILE PRO ALA PRO PRO LEU SEQRES 2 C 178 SER LYS VAL PRO LEU GLN GLN ASN PHE GLN ASP ASN GLN SEQRES 3 C 178 PHE GLN GLY LYS TRP TYR VAL VAL GLY LEU ALA GLY ASN SEQRES 4 C 178 ALA ILE LEU ARG GLU ASP LYS ASP PRO GLN LYS MET TYR SEQRES 5 C 178 ALA THR ILE TYR GLU LEU LYS GLU ASP LYS SER TYR ASN SEQRES 6 C 178 VAL THR SER VAL LEU PHE ARG LYS LYS LYS CYS ASP TYR SEQRES 7 C 178 TRP ILE ARG THR PHE VAL PRO GLY SER GLN PRO GLY GLU SEQRES 8 C 178 PHE THR LEU GLY ASN ILE LYS SER TYR PRO GLY LEU THR SEQRES 9 C 178 SER TYR LEU VAL ARG VAL VAL SER THR ASN TYR ASN GLN SEQRES 10 C 178 HIS ALA MET VAL PHE PHE LYS LYS VAL SER GLN ASN ARG SEQRES 11 C 178 GLU TYR PHE LYS ILE THR LEU TYR GLY ARG THR LYS GLU SEQRES 12 C 178 LEU THR SER GLU LEU LYS GLU ASN PHE ILE ARG PHE SER SEQRES 13 C 178 LYS SER LEU GLY LEU PRO GLU ASN HIS ILE VAL PHE PRO SEQRES 14 C 178 VAL PRO ILE ASP GLN CYS ILE ASP GLY HET CM1 A 200 54 HET CM1 B 200 54 HET CM1 C 200 54 HETNAM CM1 CARBOXYMYCOBACTIN S FORMUL 4 CM1 3(C36 H51 FE N5 O12) FORMUL 7 HOH *95(H2 O) HELIX 1 1 PRO A 12 VAL A 16 5 5 HELIX 2 2 GLN A 23 GLN A 28 1 6 HELIX 3 3 ASN A 96 TYR A 100 5 5 HELIX 4 4 THR A 145 SER A 158 1 14 HELIX 5 5 PRO A 162 ASN A 164 5 3 HELIX 6 6 PRO B 12 VAL B 16 5 5 HELIX 7 7 GLN B 23 GLN B 28 1 6 HELIX 8 8 ASN B 96 TYR B 100 5 5 HELIX 9 9 THR B 145 SER B 158 1 14 HELIX 10 10 PRO B 162 ASN B 164 5 3 HELIX 11 11 PRO C 12 VAL C 16 5 5 HELIX 12 12 GLN C 23 GLN C 28 1 6 HELIX 13 13 ASN C 96 TYR C 100 5 5 HELIX 14 14 THR C 145 LEU C 159 1 15 HELIX 15 15 PRO C 162 ASN C 164 5 3 SHEET 1 A10 ILE A 166 VAL A 167 0 SHEET 2 A10 GLY A 29 GLY A 38 -1 N LEU A 36 O VAL A 167 SHEET 3 A10 ARG A 130 GLY A 139 -1 O GLY A 139 N TYR A 32 SHEET 4 A10 HIS A 118 SER A 127 -1 N ALA A 119 O TYR A 138 SHEET 5 A10 LEU A 103 THR A 113 -1 N ARG A 109 O PHE A 122 SHEET 6 A10 GLU A 91 LEU A 94 -1 N PHE A 92 O VAL A 108 SHEET 7 A10 LYS A 75 PRO A 85 -1 N VAL A 84 O THR A 93 SHEET 8 A10 TYR A 64 ARG A 72 -1 N VAL A 66 O ARG A 81 SHEET 9 A10 ALA A 53 LEU A 58 -1 N ILE A 55 O THR A 67 SHEET 10 A10 GLY A 29 GLY A 38 -1 N GLY A 29 O TYR A 56 SHEET 1 B10 ILE B 166 VAL B 167 0 SHEET 2 B10 GLY B 29 GLY B 38 -1 N LEU B 36 O VAL B 167 SHEET 3 B10 ARG B 130 GLY B 139 -1 O GLY B 139 N TYR B 32 SHEET 4 B10 HIS B 118 SER B 127 -1 N ALA B 119 O TYR B 138 SHEET 5 B10 LEU B 103 THR B 113 -1 N SER B 112 O MET B 120 SHEET 6 B10 GLU B 91 LEU B 94 -1 N PHE B 92 O VAL B 108 SHEET 7 B10 LYS B 75 PRO B 85 -1 N VAL B 84 O THR B 93 SHEET 8 B10 TYR B 64 ARG B 72 -1 N SER B 68 O TRP B 79 SHEET 9 B10 ALA B 53 LEU B 58 -1 N ILE B 55 O THR B 67 SHEET 10 B10 GLY B 29 GLY B 38 -1 N GLY B 29 O TYR B 56 SHEET 1 C10 ILE C 166 VAL C 167 0 SHEET 2 C10 GLY C 29 GLY C 38 -1 N LEU C 36 O VAL C 167 SHEET 3 C10 ARG C 130 GLY C 139 -1 O GLY C 139 N TYR C 32 SHEET 4 C10 HIS C 118 SER C 127 -1 N ALA C 119 O TYR C 138 SHEET 5 C10 LEU C 103 THR C 113 -1 N ARG C 109 O PHE C 122 SHEET 6 C10 GLU C 91 LEU C 94 -1 N PHE C 92 O VAL C 108 SHEET 7 C10 LYS C 75 PRO C 85 -1 N VAL C 84 O THR C 93 SHEET 8 C10 TYR C 64 ARG C 72 -1 N VAL C 66 O ARG C 81 SHEET 9 C10 ALA C 53 LEU C 58 -1 N ILE C 55 O THR C 67 SHEET 10 C10 GLY C 29 GLY C 38 -1 N GLY C 29 O TYR C 56 SSBOND 1 CYS A 76 CYS A 175 1555 1555 2.04 SSBOND 2 CYS B 76 CYS B 175 1555 1555 2.04 SSBOND 3 CYS C 76 CYS C 175 1555 1555 2.07 SITE 1 AC1 11 TYR A 52 THR A 54 SER A 68 LEU A 70 SITE 2 AC1 11 ARG A 72 TRP A 79 ARG A 81 PHE A 123 SITE 3 AC1 11 LYS A 125 LYS A 134 TYR A 138 SITE 1 AC2 10 TYR B 52 THR B 54 SER B 68 LEU B 70 SITE 2 AC2 10 TRP B 79 ARG B 81 PHE B 123 LYS B 125 SITE 3 AC2 10 LYS B 134 TYR B 138 SITE 1 AC3 12 TYR C 52 THR C 54 SER C 68 LEU C 70 SITE 2 AC3 12 ARG C 72 TRP C 79 ARG C 81 PHE C 123 SITE 3 AC3 12 LYS C 125 PHE C 133 LYS C 134 TYR C 138 CRYST1 114.200 114.200 119.300 90.00 90.00 90.00 P 41 21 2 24 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 0.008757 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008757 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008382 0.00000