10 20 30 40 50 60 70 80 3DSZ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER TRANSPORT PROTEIN 14-JUL-08 3DSZ
TITLE ENGINEERED HUMAN LIPOCALIN 2 IN COMPLEX WITH Y-DTPA
COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENGINEERED HUMAN LIPOCALIN 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: NEUTROPHIL GELATINASE-ASSOCIATED LIPOCALIN, NGAL, COMPND 5 SIDEROCALIN; COMPND 6 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, VARIANT TB7.N9; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PNGAL15
KEYWDS PROTEIN DESIGN, LIGAND BINDING PROTEIN, BETA BARREL, KEYWDS 2 ENGINEERED LIPOCALIN, DE NOVO PROTEIN, PROTEIN BINDING, KEYWDS 3 TRANSPORT PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR A.EICHINGER,A.SKERRA
REVDAT 1 19-MAY-09 3DSZ 0
JRNL AUTH H.J.KIM,A.EICHINGER,A.SKERRA JRNL TITL HIGH-AFFINITY RECOGNITION OF LANTHANIDE(III) JRNL TITL 2 CHELATE COMPLEXES BY A REPROGRAMMED HUMAN JRNL TITL 3 LIPOCALIN 2 JRNL REF J.AM.CHEM.SOC. V. 131 3565 2009 JRNL REFN ISSN 0002-7863 JRNL PMID 19227970 JRNL DOI 10.1021/JA806857R
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 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) (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 26807 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1347 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 2788 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 100 REMARK 3 SOLVENT ATOMS : 328 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.18400 REMARK 3 B22 (A**2) : 2.18400 REMARK 3 B33 (A**2) : -4.36700 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.402 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.187 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.172 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.331 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 56.91 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.PARAM REMARK 3 PARAMETER FILE 3 : DTPA-TRIS-NOY.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 3DSZ COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUL-08. REMARK 100 THE RCSB ID CODE IS RCSB048449.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-MAR-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95373 REMARK 200 MONOCHROMATOR : SI 111 CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26827 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 66.979 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 9.700 REMARK 200 R MERGE (I) : 0.10900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 4.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.4 REMARK 200 DATA REDUNDANCY IN SHELL : 9.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37200 REMARK 200 R SYM FOR SHELL (I) : 0.37200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.100 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 (%): 46.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% POLYETHYLENE GLYCOL 3350, 0.1M REMARK 280 BISTRIS/HCL, PH5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K
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 57.56400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 41.17500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 41.17500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.78200 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 41.17500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 41.17500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 86.34600 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 41.17500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 41.17500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.78200 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 41.17500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 41.17500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 86.34600 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 57.56400 REMARK 290 REMARK 290 REMARK: NULL
REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 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 THR A 4 REMARK 465 SER A 5 REMARK 465 ASP A 6 REMARK 465 SER A 179 REMARK 465 ALA A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 GLN B 1 REMARK 465 ASP B 2 REMARK 465 SER B 3 REMARK 465 THR B 4 REMARK 465 SER B 5 REMARK 465 SER B 179 REMARK 465 ALA B 180 REMARK 465 HIS B 181 REMARK 465 HIS B 182 REMARK 465 HIS B 183 REMARK 465 HIS B 184 REMARK 465 HIS B 185 REMARK 465 HIS B 186
REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ALA A 41 REMARK 475 ALA B 41
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 B 329 O HOH B 385 0.00 REMARK 500 N LYS A 46 O HOH A 325 2.14 REMARK 500 OH TYR B 32 OD2 ASP B 177 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 343 O HOH A 343 7466 1.25 REMARK 500 ND2 ASN A 116 ND2 ASN A 116 8666 1.60 REMARK 500 NZ LYS A 46 O SER A 99 3555 1.70 REMARK 500 O ASP A 177 O HOH B 323 5546 1.99 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 ASP A 45 N - CA - CB ANGL. DEV. = -12.9 DEGREES REMARK 500 ARG B 140 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG B 140 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ASP B 177 C - N - CA ANGL. DEV. = -22.6 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 ALA A 41 161.14 -29.78 REMARK 500 ARG A 43 112.51 56.58 REMARK 500 ASP A 45 114.56 -165.51 REMARK 500 LYS A 46 39.40 -88.38 REMARK 500 TYR A 115 -32.79 66.06 REMARK 500 GLN A 117 -56.38 -131.37 REMARK 500 ASN A 129 19.24 59.83 REMARK 500 CYS A 175 -50.73 68.57 REMARK 500 ALA B 41 -76.95 -81.40 REMARK 500 LEU B 42 114.57 27.25 REMARK 500 GLU B 44 -11.54 -49.52 REMARK 500 TYR B 115 -37.47 61.43 REMARK 500 GLN B 117 -54.29 -138.02 REMARK 500 CYS B 175 -41.85 66.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 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: (11X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ARG A 43 24.1 L L OUTSIDE RANGE REMARK 500 ASP B 177 16.4 L L OUTSIDE RANGE 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 327 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A 332 DISTANCE = 5.09 ANGSTROMS REMARK 525 HOH A 333 DISTANCE = 6.81 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LIZ A 187 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LIZ B 187 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 B 188 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE YT3 A 188
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3DTQ RELATED DB: PDB REMARK 900 ENGINEERED HUMAN LIPOCALIN 2 WITH SPECIFICITY FOR Y-DTPA, REMARK 900 APO-FORM REMARK 900 RELATED ID: 1L6M RELATED DB: PDB REMARK 900 NATIVE HUMAN LIPOCALIN 2
REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN REMARK 999 DOES NOT CURRENTLY EXIST. REMARK 999 THIS SEQUENCE WILL BE DEPOSITED IN THE SEQUENCE DATABASE.
DBREF 3DSZ A 1 186 PDB 3DSZ 3DSZ 1 186 DBREF 3DSZ B 1 186 PDB 3DSZ 3DSZ 1 186
SEQRES 1 A 186 GLN ASP SER THR SER ASP LEU ILE PRO ALA PRO PRO LEU SEQRES 2 A 186 SER LYS VAL PRO LEU GLN GLN ASN PHE GLN ASP ASN GLN SEQRES 3 A 186 PHE HIS GLY LYS TRP TYR GLN VAL GLY ARG ALA GLY ASN SEQRES 4 A 186 ALA ALA LEU ARG GLU ASP LYS ASP PRO GLN LYS MET THR SEQRES 5 A 186 ALA GLN ILE TYR GLU LEU LYS GLU ASP LYS SER TYR ASN SEQRES 6 A 186 VAL THR ALA VAL ARG PHE ARG LYS LYS LYS CYS ASP TYR SEQRES 7 A 186 LEU THR MET THR PHE VAL PRO GLY SER GLN PRO GLY GLU SEQRES 8 A 186 PHE THR LEU GLY ASN ILE LYS SER TYR PRO GLY LEU THR SEQRES 9 A 186 SER TYR LEU VAL ARG VAL VAL SER THR ASN TYR ASN GLN SEQRES 10 A 186 HIS ALA MET VAL PHE PHE LYS LYS VAL SER GLN ASN ARG SEQRES 11 A 186 GLU TYR PHE SER ILE THR LEU LEU GLY ARG THR LYS GLU SEQRES 12 A 186 LEU ALA SER GLU LEU LYS GLU ASN PHE ILE ARG PHE SER SEQRES 13 A 186 LYS SER LEU GLY LEU PRO GLU ASN HIS ILE VAL PHE PRO SEQRES 14 A 186 VAL PRO ILE ASP GLN CYS ILE ASP GLY SER ALA HIS HIS SEQRES 15 A 186 HIS HIS HIS HIS SEQRES 1 B 186 GLN ASP SER THR SER ASP LEU ILE PRO ALA PRO PRO LEU SEQRES 2 B 186 SER LYS VAL PRO LEU GLN GLN ASN PHE GLN ASP ASN GLN SEQRES 3 B 186 PHE HIS GLY LYS TRP TYR GLN VAL GLY ARG ALA GLY ASN SEQRES 4 B 186 ALA ALA LEU ARG GLU ASP LYS ASP PRO GLN LYS MET THR SEQRES 5 B 186 ALA GLN ILE TYR GLU LEU LYS GLU ASP LYS SER TYR ASN SEQRES 6 B 186 VAL THR ALA VAL ARG PHE ARG LYS LYS LYS CYS ASP TYR SEQRES 7 B 186 LEU THR MET THR PHE VAL PRO GLY SER GLN PRO GLY GLU SEQRES 8 B 186 PHE THR LEU GLY ASN ILE LYS SER TYR PRO GLY LEU THR SEQRES 9 B 186 SER TYR LEU VAL ARG VAL VAL SER THR ASN TYR ASN GLN SEQRES 10 B 186 HIS ALA MET VAL PHE PHE LYS LYS VAL SER GLN ASN ARG SEQRES 11 B 186 GLU TYR PHE SER ILE THR LEU LEU GLY ARG THR LYS GLU SEQRES 12 B 186 LEU ALA SER GLU LEU LYS GLU ASN PHE ILE ARG PHE SER SEQRES 13 B 186 LYS SER LEU GLY LEU PRO GLU ASN HIS ILE VAL PHE PRO SEQRES 14 B 186 VAL PRO ILE ASP GLN CYS ILE ASP GLY SER ALA HIS HIS SEQRES 15 B 186 HIS HIS HIS HIS
HET LIZ A 187 49 HET YT3 A 188 1 HET LIZ B 187 49 HET YT3 B 188 1
HETNAM LIZ N-{(1S,2S)-2-[BIS(CARBOXYMETHYL)AMINO]CYCLOHEXYL}-N- HETNAM 2 LIZ {(2R)-2-[BIS(CARBOXYMETHYL)AMINO]-3-[4-({[2-HYDROXY-1, HETNAM 3 LIZ 1-BIS(HYDROXYMETHYL)ETHYL]CARBAMOTHIOYL}AMINO) HETNAM 4 LIZ PHENYL]PROPYL}GLYCINE HETNAM YT3 YTTRIUM (III) ION
FORMUL 3 LIZ 2(C30 H45 N5 O13 S) FORMUL 4 YT3 2(Y 3+) FORMUL 7 HOH *328(H2 O)
HELIX 1 1 PRO A 12 VAL A 16 5 5 HELIX 2 2 GLN A 23 HIS A 28 1 6 HELIX 3 3 ASN A 96 TYR A 100 5 5 HELIX 4 4 ALA 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 HIS B 28 1 6 HELIX 8 8 LEU B 42 ASP B 47 5 6 HELIX 9 9 ASN B 96 TYR B 100 5 5 HELIX 10 10 ALA B 145 LEU B 159 1 15 HELIX 11 11 PRO B 162 ASN B 164 5 3
SHEET 1 A10 ILE A 166 VAL A 167 0 SHEET 2 A10 GLY A 29 GLY A 38 -1 N ARG A 36 O VAL A 167 SHEET 3 A10 ARG A 130 GLY A 139 -1 O LEU A 137 N GLY A 35 SHEET 4 A10 HIS A 118 SER A 127 -1 N LYS A 125 O TYR A 132 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 MET 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 TRP A 31 O GLN A 54 SHEET 1 B10 ILE B 166 VAL B 167 0 SHEET 2 B10 GLY B 29 GLY B 38 -1 N ARG B 36 O VAL B 167 SHEET 3 B10 ARG B 130 GLY B 139 -1 O LEU B 137 N GLY B 35 SHEET 4 B10 HIS B 118 SER B 127 -1 N LYS B 125 O TYR B 132 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 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 VAL B 66 O MET 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 TRP B 31 O GLN B 54
SSBOND 1 CYS A 76 CYS A 175 1555 1555 2.04 SSBOND 2 CYS B 76 CYS B 175 1555 1555 2.04
SITE 1 AC1 19 GLN A 33 ARG A 36 THR A 52 GLN A 54 SITE 2 AC1 19 ALA A 68 ARG A 70 ASP A 77 TYR A 78 SITE 3 AC1 19 LEU A 79 TYR A 106 PHE A 123 THR A 136 SITE 4 AC1 19 HOH A 189 HOH A 193 HOH A 197 HOH A 219 SITE 5 AC1 19 HOH A 323 HOH A 334 HOH A 345 SITE 1 AC2 1 HOH A 189 SITE 1 AC3 19 LYS A 73 LYS A 74 GLN B 33 ARG B 36 SITE 2 AC3 19 THR B 52 GLN B 54 ALA B 68 ARG B 70 SITE 3 AC3 19 ASP B 77 LEU B 79 TYR B 106 PHE B 123 SITE 4 AC3 19 THR B 136 HOH B 223 HOH B 231 HOH B 237 SITE 5 AC3 19 HOH B 263 HOH B 280 HOH B 296 SITE 1 AC4 1 HOH B 223
CRYST1 82.350 82.350 115.128 90.00 90.00 90.00 P 41 21 2 16
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 0.012143 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012143 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008686 0.00000