HEADER LIGAND BINDING PROTEIN 15-JAN-08 3BY0 TITLE CRYSTAL STRUCTURE OF SIDEROCALIN (NGAL, LIPOCALIN 2) W79A-R81A TITLE 2 COMPLEXED WITH FERRIC ENTEROBACTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN; COMPND 3 CHAIN: A, B, C; COMPND 4 SYNONYM: NGAL; P25; 25 KDA ALPHA-2-MICROGLOBULIN-RELATED SUBUNIT OF COMPND 5 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 GENE: LCN2, NGAL, HNL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS RIL; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-3 KEYWDS BETA BARREL, LIGAND BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.C.CLIFTON,J.C.PIZZARO,R.K.STRONG REVDAT 5 30-AUG-23 3BY0 1 REMARK REVDAT 4 20-OCT-21 3BY0 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 3BY0 1 VERSN REVDAT 2 24-FEB-09 3BY0 1 VERSN REVDAT 1 09-SEP-08 3BY0 0 JRNL AUTH R.J.ABERGEL,M.C.CLIFTON,J.C.PIZARRO,J.A.WARNER,D.K.SHUH, JRNL AUTH 2 R.K.STRONG,K.N.RAYMOND JRNL TITL THE SIDEROCALIN/ENTEROBACTIN INTERACTION: A LINK BETWEEN JRNL TITL 2 MAMMALIAN IMMUNITY AND BACTERIAL IRON TRANSPORT. JRNL REF J.AM.CHEM.SOC. V. 130 11524 2008 JRNL REFN ISSN 0002-7863 JRNL PMID 18680288 JRNL DOI 10.1021/JA803524W REMARK 2 REMARK 2 RESOLUTION. 2.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2 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) : 2.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 23194 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 + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.400 REMARK 3 FREE R VALUE TEST SET COUNT : 2410 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) : 2.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1603 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.3570 REMARK 3 BIN FREE R VALUE SET COUNT : 170 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4162 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 126 REMARK 3 SOLVENT ATOMS : 78 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 63.39 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -0.93000 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): 0.584 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.304 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.212 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.679 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.916 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4424 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3023 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6000 ; 0.840 ; 1.991 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7377 ; 0.820 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 524 ; 4.795 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 201 ;36.195 ;24.627 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 741 ;15.186 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;17.843 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 641 ; 0.053 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4843 ; 0.002 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 891 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 540 ; 0.176 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2746 ; 0.207 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1995 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2402 ; 0.078 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 139 ; 0.111 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.213 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 12 ; 0.101 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 40 ; 0.188 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 9 ; 0.071 ; 0.200 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): 2813 ; 0.456 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1037 ; 0.090 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4254 ; 0.582 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2031 ; 0.668 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1741 ; 0.991 ; 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 3BY0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-08. REMARK 100 THE DEPOSITION ID IS D_1000046097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23194 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.572 REMARK 200 RESOLUTION RANGE LOW (A) : 28.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.60 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.2890 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.50 REMARK 200 R MERGE FOR SHELL (I) : 0.39700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 7.100 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1L6M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 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 291K 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 59.52100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 57.17900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 57.17900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 29.76050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 57.17900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 57.17900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 89.28150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 57.17900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 57.17900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 29.76050 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 57.17900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.17900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 89.28150 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 59.52100 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 SUBUNIT IS A DIMER, BUT DIMERIZATION WAS REMARK 300 PREVENTED BY INTRODUCING A C87S MUTATION. 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A -19 REMARK 465 PRO A -18 REMARK 465 LEU A -17 REMARK 465 GLY A -16 REMARK 465 LEU A -15 REMARK 465 LEU A -14 REMARK 465 TRP A -13 REMARK 465 LEU A -12 REMARK 465 GLY A -11 REMARK 465 LEU A -10 REMARK 465 ALA A -9 REMARK 465 LEU A -8 REMARK 465 LEU A -7 REMARK 465 GLY A -6 REMARK 465 ALA A -5 REMARK 465 LEU A -4 REMARK 465 HIS A -3 REMARK 465 ALA A -2 REMARK 465 GLN A -1 REMARK 465 ALA A 0 REMARK 465 GLN A 1 REMARK 465 ASP A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 MET B -19 REMARK 465 PRO B -18 REMARK 465 LEU B -17 REMARK 465 GLY B -16 REMARK 465 LEU B -15 REMARK 465 LEU B -14 REMARK 465 TRP B -13 REMARK 465 LEU B -12 REMARK 465 GLY B -11 REMARK 465 LEU B -10 REMARK 465 ALA B -9 REMARK 465 LEU B -8 REMARK 465 LEU B -7 REMARK 465 GLY B -6 REMARK 465 ALA B -5 REMARK 465 LEU B -4 REMARK 465 HIS B -3 REMARK 465 ALA B -2 REMARK 465 GLN B -1 REMARK 465 ALA B 0 REMARK 465 GLN B 1 REMARK 465 ASP B 2 REMARK 465 SER B 3 REMARK 465 THR B 4 REMARK 465 ASP B 61 REMARK 465 LYS B 62 REMARK 465 ARG B 72 REMARK 465 MET C -19 REMARK 465 PRO C -18 REMARK 465 LEU C -17 REMARK 465 GLY C -16 REMARK 465 LEU C -15 REMARK 465 LEU C -14 REMARK 465 TRP C -13 REMARK 465 LEU C -12 REMARK 465 GLY C -11 REMARK 465 LEU C -10 REMARK 465 ALA C -9 REMARK 465 LEU C -8 REMARK 465 LEU C -7 REMARK 465 GLY C -6 REMARK 465 ALA C -5 REMARK 465 LEU C -4 REMARK 465 HIS C -3 REMARK 465 ALA C -2 REMARK 465 GLN C -1 REMARK 465 ALA C 0 REMARK 465 GLN C 1 REMARK 465 ASP C 2 REMARK 465 SER C 3 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 98 CB CG CD CE NZ REMARK 470 GLN A 117 CG CD OE1 NE2 REMARK 470 GLU B 60 CB CG CD OE1 OE2 REMARK 470 LYS B 73 CG CD CE NZ REMARK 470 LYS B 74 CG CD CE NZ REMARK 470 LYS B 75 CD CE NZ REMARK 470 LYS B 98 CD CE NZ REMARK 470 GLU C 60 CD OE1 OE2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLN B 117 CG CD OE1 NE2 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 TYR A 115 -38.72 73.32 REMARK 500 GLN A 117 -49.12 -131.52 REMARK 500 CYS A 175 -40.32 70.30 REMARK 500 TYR B 115 -49.86 73.22 REMARK 500 GLN B 117 -54.55 -132.31 REMARK 500 ASN B 129 -3.19 60.80 REMARK 500 CYS B 175 -57.73 68.29 REMARK 500 LYS C 62 1.24 83.22 REMARK 500 TYR C 115 -39.79 75.01 REMARK 500 GLN C 117 -58.24 -125.53 REMARK 500 CYS C 175 -40.81 76.00 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 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DBS A 191 O4 REMARK 620 2 DBS A 191 O1 77.5 REMARK 620 3 DBH A 192 O6 97.4 107.0 REMARK 620 4 DBH A 193 O3 110.1 161.0 89.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 402 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DBH B 201 O3 REMARK 620 2 DBH B 201 O6 72.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE C 403 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DBS C 301 O1 REMARK 620 2 DBS C 301 O4 75.2 REMARK 620 3 DBS C 302 O1 169.4 101.0 REMARK 620 4 DBS C 302 O4 96.1 112.6 76.0 REMARK 620 5 DBH C 303 O3 100.5 161.5 86.2 85.6 REMARK 620 6 DBH C 303 O6 102.6 86.5 86.9 156.3 76.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 531 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 532 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DBS A 191 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DBH A 192 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DBH A 193 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DBH B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DBS C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DBS C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DBH C 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 603 DBREF 3BY0 A -19 178 UNP P80188 NGAL_HUMAN 1 198 DBREF 3BY0 B -19 178 UNP P80188 NGAL_HUMAN 1 198 DBREF 3BY0 C -19 178 UNP P80188 NGAL_HUMAN 1 198 SEQADV 3BY0 ALA A 79 UNP P80188 TRP 99 ENGINEERED MUTATION SEQADV 3BY0 ALA A 81 UNP P80188 ARG 101 ENGINEERED MUTATION SEQADV 3BY0 SER A 87 UNP P80188 CYS 107 ENGINEERED MUTATION SEQADV 3BY0 ALA B 79 UNP P80188 TRP 99 ENGINEERED MUTATION SEQADV 3BY0 ALA B 81 UNP P80188 ARG 101 ENGINEERED MUTATION SEQADV 3BY0 SER B 87 UNP P80188 CYS 107 ENGINEERED MUTATION SEQADV 3BY0 ALA C 79 UNP P80188 TRP 99 ENGINEERED MUTATION SEQADV 3BY0 ALA C 81 UNP P80188 ARG 101 ENGINEERED MUTATION SEQADV 3BY0 SER C 87 UNP P80188 CYS 107 ENGINEERED MUTATION SEQRES 1 A 198 MET PRO LEU GLY LEU LEU TRP LEU GLY LEU ALA LEU LEU SEQRES 2 A 198 GLY ALA LEU HIS ALA GLN ALA GLN ASP SER THR SER ASP SEQRES 3 A 198 LEU ILE PRO ALA PRO PRO LEU SER LYS VAL PRO LEU GLN SEQRES 4 A 198 GLN ASN PHE GLN ASP ASN GLN PHE GLN GLY LYS TRP TYR SEQRES 5 A 198 VAL VAL GLY LEU ALA GLY ASN ALA ILE LEU ARG GLU ASP SEQRES 6 A 198 LYS ASP PRO GLN LYS MET TYR ALA THR ILE TYR GLU LEU SEQRES 7 A 198 LYS GLU ASP LYS SER TYR ASN VAL THR SER VAL LEU PHE SEQRES 8 A 198 ARG LYS LYS LYS CYS ASP TYR ALA ILE ALA THR PHE VAL SEQRES 9 A 198 PRO GLY SER GLN PRO GLY GLU PHE THR LEU GLY ASN ILE SEQRES 10 A 198 LYS SER TYR PRO GLY LEU THR SER TYR LEU VAL ARG VAL SEQRES 11 A 198 VAL SER THR ASN TYR ASN GLN HIS ALA MET VAL PHE PHE SEQRES 12 A 198 LYS LYS VAL SER GLN ASN ARG GLU TYR PHE LYS ILE THR SEQRES 13 A 198 LEU TYR GLY ARG THR LYS GLU LEU THR SER GLU LEU LYS SEQRES 14 A 198 GLU ASN PHE ILE ARG PHE SER LYS SER LEU GLY LEU PRO SEQRES 15 A 198 GLU ASN HIS ILE VAL PHE PRO VAL PRO ILE ASP GLN CYS SEQRES 16 A 198 ILE ASP GLY SEQRES 1 B 198 MET PRO LEU GLY LEU LEU TRP LEU GLY LEU ALA LEU LEU SEQRES 2 B 198 GLY ALA LEU HIS ALA GLN ALA GLN ASP SER THR SER ASP SEQRES 3 B 198 LEU ILE PRO ALA PRO PRO LEU SER LYS VAL PRO LEU GLN SEQRES 4 B 198 GLN ASN PHE GLN ASP ASN GLN PHE GLN GLY LYS TRP TYR SEQRES 5 B 198 VAL VAL GLY LEU ALA GLY ASN ALA ILE LEU ARG GLU ASP SEQRES 6 B 198 LYS ASP PRO GLN LYS MET TYR ALA THR ILE TYR GLU LEU SEQRES 7 B 198 LYS GLU ASP LYS SER TYR ASN VAL THR SER VAL LEU PHE SEQRES 8 B 198 ARG LYS LYS LYS CYS ASP TYR ALA ILE ALA THR PHE VAL SEQRES 9 B 198 PRO GLY SER GLN PRO GLY GLU PHE THR LEU GLY ASN ILE SEQRES 10 B 198 LYS SER TYR PRO GLY LEU THR SER TYR LEU VAL ARG VAL SEQRES 11 B 198 VAL SER THR ASN TYR ASN GLN HIS ALA MET VAL PHE PHE SEQRES 12 B 198 LYS LYS VAL SER GLN ASN ARG GLU TYR PHE LYS ILE THR SEQRES 13 B 198 LEU TYR GLY ARG THR LYS GLU LEU THR SER GLU LEU LYS SEQRES 14 B 198 GLU ASN PHE ILE ARG PHE SER LYS SER LEU GLY LEU PRO SEQRES 15 B 198 GLU ASN HIS ILE VAL PHE PRO VAL PRO ILE ASP GLN CYS SEQRES 16 B 198 ILE ASP GLY SEQRES 1 C 198 MET PRO LEU GLY LEU LEU TRP LEU GLY LEU ALA LEU LEU SEQRES 2 C 198 GLY ALA LEU HIS ALA GLN ALA GLN ASP SER THR SER ASP SEQRES 3 C 198 LEU ILE PRO ALA PRO PRO LEU SER LYS VAL PRO LEU GLN SEQRES 4 C 198 GLN ASN PHE GLN ASP ASN GLN PHE GLN GLY LYS TRP TYR SEQRES 5 C 198 VAL VAL GLY LEU ALA GLY ASN ALA ILE LEU ARG GLU ASP SEQRES 6 C 198 LYS ASP PRO GLN LYS MET TYR ALA THR ILE TYR GLU LEU SEQRES 7 C 198 LYS GLU ASP LYS SER TYR ASN VAL THR SER VAL LEU PHE SEQRES 8 C 198 ARG LYS LYS LYS CYS ASP TYR ALA ILE ALA THR PHE VAL SEQRES 9 C 198 PRO GLY SER GLN PRO GLY GLU PHE THR LEU GLY ASN ILE SEQRES 10 C 198 LYS SER TYR PRO GLY LEU THR SER TYR LEU VAL ARG VAL SEQRES 11 C 198 VAL SER THR ASN TYR ASN GLN HIS ALA MET VAL PHE PHE SEQRES 12 C 198 LYS LYS VAL SER GLN ASN ARG GLU TYR PHE LYS ILE THR SEQRES 13 C 198 LEU TYR GLY ARG THR LYS GLU LEU THR SER GLU LEU LYS SEQRES 14 C 198 GLU ASN PHE ILE ARG PHE SER LYS SER LEU GLY LEU PRO SEQRES 15 C 198 GLU ASN HIS ILE VAL PHE PRO VAL PRO ILE ASP GLN CYS SEQRES 16 C 198 ILE ASP GLY HET FE A 401 1 HET SO4 A 531 5 HET DBS A 191 17 HET DBH A 192 11 HET DBH A 193 11 HET GOL A 601 6 HET FE B 402 1 HET DBH B 201 11 HET FE C 403 1 HET SO4 C 532 5 HET DBS C 301 17 HET DBS C 302 17 HET DBH C 303 11 HET GOL C 602 6 HET GOL C 603 6 HETNAM FE FE (III) ION HETNAM SO4 SULFATE ION HETNAM DBS 2-(2,3-DIHYDROXY-BENZOYLAMINO)-3-HYDROXY-PROPIONIC ACID HETNAM DBH 2,3-DIHYDROXY-BENZOIC ACID HETNAM GOL GLYCEROL HETSYN DBS 2,3,-DIHYDROXYBENZOYLSERINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 FE 3(FE 3+) FORMUL 5 SO4 2(O4 S 2-) FORMUL 6 DBS 3(C10 H11 N O6) FORMUL 7 DBH 4(C7 H6 O4) FORMUL 9 GOL 3(C3 H8 O3) FORMUL 19 HOH *78(H2 O) HELIX 1 1 PRO A 12 VAL A 16 5 5 HELIX 2 2 ASN A 96 TYR A 100 5 5 HELIX 3 3 THR A 145 LEU A 159 1 15 HELIX 4 4 PRO A 162 ASN A 164 5 3 HELIX 5 5 PRO B 12 VAL B 16 5 5 HELIX 6 6 GLN B 23 GLN B 28 1 6 HELIX 7 7 ASN B 96 TYR B 100 5 5 HELIX 8 8 THR B 145 SER B 158 1 14 HELIX 9 9 PRO B 162 ASN B 164 5 3 HELIX 10 10 PRO C 12 VAL C 16 5 5 HELIX 11 11 GLN C 23 GLN C 28 1 6 HELIX 12 12 ASN C 96 TYR C 100 5 5 HELIX 13 13 THR C 145 LEU C 159 1 15 HELIX 14 14 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 ALA 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 ARG B 109 O PHE B 122 SHEET 6 B10 GLU B 91 LEU B 94 -1 N PHE B 92 O VAL B 108 SHEET 7 B10 ASP B 77 PRO B 85 -1 N VAL B 84 O THR B 93 SHEET 8 B10 TYR B 64 LEU B 70 -1 N VAL B 66 O ALA B 81 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 LEU C 70 O ASP C 77 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 2.03 SSBOND 2 CYS B 76 CYS B 175 1555 1555 2.03 SSBOND 3 CYS C 76 CYS C 175 1555 1555 2.04 LINK O4 DBS A 191 FE FE A 401 1555 1555 2.23 LINK O1 DBS A 191 FE FE A 401 1555 1555 2.12 LINK O6 DBH A 192 FE FE A 401 1555 1555 2.06 LINK O3 DBH A 193 FE FE A 401 1555 1555 1.74 LINK O3 DBH B 201 FE FE B 402 1555 1555 2.22 LINK O6 DBH B 201 FE FE B 402 1555 1555 2.42 LINK O1 DBS C 301 FE FE C 403 1555 1555 2.09 LINK O4 DBS C 301 FE FE C 403 1555 1555 2.34 LINK O1 DBS C 302 FE FE C 403 1555 1555 1.76 LINK O4 DBS C 302 FE FE C 403 1555 1555 2.53 LINK O3 DBH C 303 FE FE C 403 1555 1555 2.22 LINK O6 DBH C 303 FE FE C 403 1555 1555 2.21 CISPEP 1 LYS B 73 LYS B 74 0 -6.23 SITE 1 AC3 3 ASN A 164 HIS A 165 LYS C 75 SITE 1 AC4 4 LYS A 75 PRO C 162 ASN C 164 HIS C 165 SITE 1 AC5 6 ALA A 40 TYR A 106 PHE A 123 LYS A 125 SITE 2 AC5 6 TYR A 132 LYS A 134 SITE 1 AC6 2 SER A 68 LYS A 134 SITE 1 AC7 5 ALA A 81 TYR A 100 LEU A 103 TYR A 106 SITE 2 AC7 5 LYS A 125 SITE 1 AC8 3 ALA B 40 TYR B 106 LYS B 134 SITE 1 AC9 6 ILE C 41 TYR C 106 PHE C 123 LYS C 125 SITE 2 AC9 6 TYR C 132 LYS C 134 SITE 1 BC1 8 SER C 68 ALA C 79 ALA C 81 PHE C 83 SITE 2 BC1 8 LEU C 94 TYR C 100 TYR C 106 LYS C 125 SITE 1 BC2 2 ARG C 72 LYS C 134 SITE 1 BC3 3 ASN A 114 HIS A 118 ASN B 116 SITE 1 BC4 4 THR C 93 LEU C 94 SER C 105 TYR C 106 SITE 1 BC5 3 LYS C 59 GLU C 60 ASP C 61 CRYST1 114.358 114.358 119.042 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 0.008744 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008744 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008400 0.00000