HEADER ANTIMICROBIAL PROTEIN 25-OCT-10 3PED TITLE SIDEROCALIN RECOGNITIN OF CARBOXYMYCOBACTINS: INTERFERENCE BY THE TITLE 2 IMMUNE SYSTEM IN INTRACELLULAR IRON ACQUISITION BY MYCOBACTERIA TITLE 3 TUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 21 TO 198; COMPND 5 SYNONYM: SIDEROCALIN, NGAL, 25 KDA ALPHA-2-MICROGLOBULIN-RELATED COMPND 6 SUBUNIT OF MMP-9, LIPOCALIN-2, ONCOGENE 24P3, P25; COMPND 7 ENGINEERED: 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, HNL, NGAL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 8-STRANDED ANTI-PARALLEL BETA BARREL, SIDEROCALIN, SIDEROPHORE KEYWDS 2 BINDING, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.C.CLIFTON REVDAT 2 06-SEP-23 3PED 1 REMARK SEQADV LINK REVDAT 1 05-OCT-11 3PED 0 JRNL AUTH T.M.HOETTE,M.C.CLIFTON,A.M.ZAWADZKA,M.A.HOLMES,R.K.STRONG, JRNL AUTH 2 K.R.RAYMOND JRNL TITL SIDEROCALIN RECOGNITIN OF CARBOXYMYCOBACTINS: INTERFERENCE JRNL TITL 2 BY THE IMMUNE SYSTEM IN INTRACELLULAR IRON ACQUISITION BY JRNL TITL 3 MYCOBACTERIA TUBERCULOSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 32071 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 + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.500 REMARK 3 FREE R VALUE TEST SET COUNT : 3359 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2174 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 230 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4054 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 170 REMARK 3 SOLVENT ATOMS : 159 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.215 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.139 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.560 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4378 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2999 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5949 ; 1.286 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7346 ; 0.831 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 529 ; 5.890 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;34.353 ;23.851 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 688 ;14.846 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;21.969 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 651 ; 0.045 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4765 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 892 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2625 ; 0.577 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1040 ; 0.085 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4268 ; 1.076 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1753 ; 1.313 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1675 ; 2.183 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3PED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-10. REMARK 100 THE DEPOSITION ID IS D_1000062275. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : APR-09 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) : 0.97 REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL, CYLINDRICALLY REMARK 200 BENT, SI(220) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35471 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 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: REFMAC 5.5.0072 REMARK 200 STARTING MODEL: PDB ENTRY 1L6M 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): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.3M AMMONIUM SULFATE, 0.2M LITHIUM REMARK 280 SULFATE, 50MM SODIUM CHLORIDE, 0.1M SODIUM ACETATE, PH 4.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 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 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 GLN B 1 REMARK 465 ASP B 2 REMARK 465 SER B 3 REMARK 465 THR B 4 REMARK 465 ASP B 45 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 SER C 5 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 ASP A 6 OD1 OD2 REMARK 470 ARG A 43 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 44 CG CD OE1 OE2 REMARK 470 ASP A 45 CG OD1 OD2 REMARK 470 LYS A 46 CG CD CE NZ REMARK 470 ASP A 47 OD1 OD2 REMARK 470 GLU A 57 OE1 OE2 REMARK 470 GLU A 60 CG CD OE1 OE2 REMARK 470 ASN A 65 CG OD1 ND2 REMARK 470 ARG A 72 CZ NH1 NH2 REMARK 470 LYS A 73 CE NZ REMARK 470 LYS A 74 CD CE NZ REMARK 470 ASN A 96 OD1 ND2 REMARK 470 LYS A 98 CG CD CE NZ REMARK 470 GLN A 117 OE1 NE2 REMARK 470 LYS A 124 CE NZ REMARK 470 GLN A 128 OE1 NE2 REMARK 470 ARG A 130 NH1 NH2 REMARK 470 GLU A 143 OE1 OE2 REMARK 470 GLU A 147 OE1 OE2 REMARK 470 GLU A 150 OE1 OE2 REMARK 470 ASN A 151 OD1 ND2 REMARK 470 ARG A 154 CZ NH1 NH2 REMARK 470 GLU A 163 CD OE1 OE2 REMARK 470 LYS B 15 NZ REMARK 470 GLN B 26 CD OE1 NE2 REMARK 470 GLN B 28 CD OE1 NE2 REMARK 470 LEU B 42 CD1 CD2 REMARK 470 ARG B 43 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 LYS B 46 CG CD CE NZ REMARK 470 ASP B 47 CG OD1 OD2 REMARK 470 LYS B 50 CE NZ REMARK 470 GLU B 60 CD OE1 OE2 REMARK 470 LEU B 70 CD1 CD2 REMARK 470 ARG B 72 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 73 CD CE NZ REMARK 470 LYS B 74 CD CE NZ REMARK 470 ILE B 80 CD1 REMARK 470 GLN B 88 CD OE1 NE2 REMARK 470 ASN B 96 OD1 ND2 REMARK 470 GLN B 117 OE1 NE2 REMARK 470 LYS B 124 CE NZ REMARK 470 GLN B 128 OE1 NE2 REMARK 470 GLU B 131 OE1 OE2 REMARK 470 GLU B 143 CG CD OE1 OE2 REMARK 470 SER B 146 OG REMARK 470 GLU B 147 CD OE1 OE2 REMARK 470 LYS B 149 CD CE NZ REMARK 470 GLU B 150 CG CD OE1 OE2 REMARK 470 ASN B 151 CG OD1 ND2 REMARK 470 ARG B 154 NH1 NH2 REMARK 470 GLU B 163 OE1 OE2 REMARK 470 ASN C 25 CG OD1 ND2 REMARK 470 ARG C 43 CZ NH1 NH2 REMARK 470 GLU C 44 CG CD OE1 OE2 REMARK 470 ASP C 45 OD1 OD2 REMARK 470 LYS C 46 CG CD CE NZ REMARK 470 ASP C 47 OD1 OD2 REMARK 470 GLU C 60 CD OE1 OE2 REMARK 470 LYS C 62 CD CE NZ REMARK 470 ARG C 72 CZ NH1 NH2 REMARK 470 LYS C 73 CD CE NZ REMARK 470 LYS C 74 CD CE NZ REMARK 470 ASN C 96 OD1 ND2 REMARK 470 LYS C 98 CE NZ REMARK 470 SER C 127 OG REMARK 470 GLN C 128 OE1 NE2 REMARK 470 GLU C 143 OE1 OE2 REMARK 470 GLU C 147 CD OE1 OE2 REMARK 470 LYS C 149 CD CE NZ REMARK 470 ARG C 154 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 157 NZ REMARK 470 GLU C 163 CG CD OE1 OE2 REMARK 470 ASP C 173 CG OD1 OD2 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 ASN A 21 63.59 38.88 REMARK 500 TYR A 115 -30.93 72.90 REMARK 500 CYS A 175 -41.34 73.80 REMARK 500 LYS B 62 10.43 80.82 REMARK 500 TYR B 115 -39.11 72.60 REMARK 500 GLN B 117 -53.35 -122.88 REMARK 500 CYS B 175 -45.79 69.11 REMARK 500 TYR C 115 -35.69 71.24 REMARK 500 GLN C 117 -52.92 -125.95 REMARK 500 ASN C 129 15.62 52.74 REMARK 500 CYS C 175 -38.67 75.59 REMARK 500 REMARK 500 REMARK: NULL 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 179 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ZYF A 200 O2 REMARK 620 2 ZYF A 200 N11 86.3 REMARK 620 3 ZYF A 200 O38 160.8 90.9 REMARK 620 4 ZYF A 200 O36 90.5 104.4 71.8 REMARK 620 5 ZYF A 200 O44 103.5 94.2 95.7 157.4 REMARK 620 6 ZYF A 200 O46 93.8 161.7 94.7 93.8 68.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 179 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ZYF B 200 O36 REMARK 620 2 ZYF B 200 O44 162.0 REMARK 620 3 ZYF B 200 O2 93.3 97.4 REMARK 620 4 ZYF B 200 O46 93.7 70.4 98.8 REMARK 620 5 ZYF B 200 N11 110.4 85.7 80.6 156.0 REMARK 620 6 ZYF B 200 O38 71.4 100.1 161.6 92.3 95.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 179 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ZYF C 200 O36 REMARK 620 2 ZYF C 200 O2 86.1 REMARK 620 3 ZYF C 200 O38 80.0 164.9 REMARK 620 4 ZYF C 200 O46 86.6 98.2 86.7 REMARK 620 5 ZYF C 200 N11 108.5 85.9 93.1 164.7 REMARK 620 6 ZYF C 200 O44 160.4 103.5 91.5 75.3 89.4 REMARK 620 7 ZYF C 200 N35 27.7 113.8 52.2 84.5 107.4 139.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE A 179 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZYF A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE B 179 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZYF B 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FE C 179 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZYF C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 180 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1X89 RELATED DB: PDB REMARK 900 RELATED ID: 1X8U RELATED DB: PDB REMARK 900 RELATED ID: 3PEC RELATED DB: PDB DBREF 3PED A 1 178 UNP P80188 NGAL_HUMAN 21 198 DBREF 3PED B 1 178 UNP P80188 NGAL_HUMAN 21 198 DBREF 3PED C 1 178 UNP P80188 NGAL_HUMAN 21 198 SEQADV 3PED SER A 87 UNP P80188 CYS 107 ENGINEERED MUTATION SEQADV 3PED SER B 87 UNP P80188 CYS 107 ENGINEERED MUTATION SEQADV 3PED 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 FE A 179 1 HET ZYF A 200 54 HET FE B 179 1 HET ZYF B 200 54 HET FE C 179 1 HET ZYF C 200 54 HET SO4 C 180 5 HETNAM FE FE (III) ION HETNAM ZYF (9Z)-11-{HYDROXY[(5S)-6-{[(1S)-3-{[(3S)-1-HYDROXY-2- HETNAM 2 ZYF OXOAZEPAN-3-YL]AMINO}-1-METHYL-3-OXOPROPYL]OXY}-5- HETNAM 3 ZYF ({[(4S)-2-(2-HYDROXYPHENYL)-4,5-DIHYDRO-1,3-OXAZOL-4- HETNAM 4 ZYF YL]CARBONYL}AMINO)-6-OXOHEXYL]AMINO}-11-OXOUNDEC-9- HETNAM 5 ZYF ENOIC ACID HETNAM SO4 SULFATE ION FORMUL 4 FE 3(FE 3+) FORMUL 5 ZYF 3(C37 H53 N5 O12) FORMUL 10 SO4 O4 S 2- FORMUL 11 HOH *159(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 LEU A 159 1 15 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 LEU B 159 1 15 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 PHE A 123 O LYS A 134 SHEET 5 A10 LEU A 103 THR A 113 -1 N LEU A 107 O LYS A 124 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 GLU A 57 O ASN A 65 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 LEU B 107 O LYS B 124 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 LEU B 70 O ASP B 77 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 ILE C 135 N ALA C 37 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 GLU C 57 O ASN C 65 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 2.03 SSBOND 3 CYS C 76 CYS C 175 1555 1555 2.06 LINK FE FE A 179 O2 ZYF A 200 1555 1555 1.99 LINK FE FE A 179 N11 ZYF A 200 1555 1555 2.24 LINK FE FE A 179 O38 ZYF A 200 1555 1555 2.24 LINK FE FE A 179 O36 ZYF A 200 1555 1555 2.27 LINK FE FE A 179 O44 ZYF A 200 1555 1555 2.28 LINK FE FE A 179 O46 ZYF A 200 1555 1555 2.28 LINK FE FE B 179 O36 ZYF B 200 1555 1555 2.02 LINK FE FE B 179 O44 ZYF B 200 1555 1555 2.16 LINK FE FE B 179 O2 ZYF B 200 1555 1555 2.18 LINK FE FE B 179 O46 ZYF B 200 1555 1555 2.31 LINK FE FE B 179 N11 ZYF B 200 1555 1555 2.34 LINK FE FE B 179 O38 ZYF B 200 1555 1555 2.43 LINK FE FE C 179 O36 ZYF C 200 1555 1555 1.98 LINK FE FE C 179 O2 ZYF C 200 1555 1555 2.05 LINK FE FE C 179 O38 ZYF C 200 1555 1555 2.11 LINK FE FE C 179 O46 ZYF C 200 1555 1555 2.14 LINK FE FE C 179 N11 ZYF C 200 1555 1555 2.15 LINK FE FE C 179 O44 ZYF C 200 1555 1555 2.15 LINK FE FE C 179 N35 ZYF C 200 1555 1555 2.80 SITE 1 AC1 1 ZYF A 200 SITE 1 AC2 14 TYR A 52 THR A 54 VAL A 66 SER A 68 SITE 2 AC2 14 LEU A 70 TRP A 79 ARG A 81 PHE A 123 SITE 3 AC2 14 LYS A 125 LYS A 134 TYR A 138 FE A 179 SITE 4 AC2 14 HOH A 182 HOH A 223 SITE 1 AC3 1 ZYF B 200 SITE 1 AC4 14 TYR B 52 THR B 54 SER B 68 TRP B 79 SITE 2 AC4 14 ARG B 81 PHE B 83 LYS B 125 PHE B 133 SITE 3 AC4 14 LYS B 134 TYR B 138 FE B 179 HOH B 184 SITE 4 AC4 14 HOH B 196 HOH B 197 SITE 1 AC5 1 ZYF C 200 SITE 1 AC6 11 TYR C 52 THR C 54 SER C 68 LEU C 70 SITE 2 AC6 11 TRP C 79 PHE C 123 LYS C 125 PHE C 133 SITE 3 AC6 11 LYS C 134 TYR C 138 FE C 179 SITE 1 AC7 4 GLN A 117 ASN C 114 HOH C 246 HOH C 252 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