HEADER HYDROLASE 13-NOV-09 3KOD TITLE DTD FROM PLASMODIUM FALCIPARUM IN COMPLEX WITH D-SERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-TYROSYL-TRNA(TYR) DEACYLASE; COMPND 3 CHAIN: A, B, C, D, E, F; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 GENE: DTD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS DTD, DEACYLASE, D-SERINE, D-AMINO ACID, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.MANICKAM,T.K.BHATT,A.SHARMA REVDAT 4 20-MAR-24 3KOD 1 REMARK REVDAT 3 01-NOV-17 3KOD 1 REMARK REVDAT 2 02-MAR-10 3KOD 1 JRNL REVDAT 1 08-DEC-09 3KOD 0 JRNL AUTH T.K.BHATT,M.YOGAVEL,S.WYDAU,R.BERWAL,A.SHARMA JRNL TITL LIGAND-BOUND STRUCTURES PROVIDE ATOMIC SNAPSHOTS FOR THE JRNL TITL 2 CATALYTIC MECHANISM OF D-AMINO ACID DEACYLASE JRNL REF J.BIOL.CHEM. V. 285 5917 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20007323 JRNL DOI 10.1074/JBC.M109.038562 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 18737 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : 0.305 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 942 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1284 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.59 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 81 REMARK 3 BIN FREE R VALUE : 0.4360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7259 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 87.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.29000 REMARK 3 B22 (A**2) : 2.78000 REMARK 3 B33 (A**2) : 2.13000 REMARK 3 B12 (A**2) : 0.17000 REMARK 3 B13 (A**2) : 5.03000 REMARK 3 B23 (A**2) : 5.35000 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): 0.609 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.525 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 28.513 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7634 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10294 ; 1.502 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 901 ; 7.493 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 380 ;45.715 ;25.474 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1434 ;21.267 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;22.782 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1151 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5655 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3921 ; 0.250 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5045 ; 0.324 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 330 ; 0.184 ; 0.200 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): 48 ; 0.234 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.227 ; 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): 4624 ; 0.635 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7359 ; 1.155 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3389 ; 1.156 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2935 ; 1.839 ; 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 3KOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000056243. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2-6.5 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 MICROMAX-007 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 : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20428 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.910 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.91 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.56600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 42.58 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 3350, 0.1M MES, PH 6.2-6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z 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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13870 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 LYS A 17 REMARK 465 GLU A 18 REMARK 465 ASN A 19 REMARK 465 ILE A 20 REMARK 465 GLY A 21 REMARK 465 GLU A 22 REMARK 465 ASN A 23 REMARK 465 GLU A 24 REMARK 465 LYS A 25 REMARK 465 ASN A 161 REMARK 465 LEU A 162 REMARK 465 ASN A 163 REMARK 465 LYS A 164 REMARK 465 ASN B 19 REMARK 465 ILE B 20 REMARK 465 GLY B 21 REMARK 465 GLU B 22 REMARK 465 LEU B 162 REMARK 465 ASN B 163 REMARK 465 LYS B 164 REMARK 465 ASN C 19 REMARK 465 ILE C 20 REMARK 465 GLY C 21 REMARK 465 GLU C 22 REMARK 465 ILE C 160 REMARK 465 ASN C 161 REMARK 465 LEU C 162 REMARK 465 ASN C 163 REMARK 465 LYS C 164 REMARK 465 GLU D 18 REMARK 465 ASN D 19 REMARK 465 ILE D 20 REMARK 465 GLY D 21 REMARK 465 GLU D 22 REMARK 465 ASN D 23 REMARK 465 GLU D 24 REMARK 465 LYS D 25 REMARK 465 ILE D 160 REMARK 465 ASN D 161 REMARK 465 LEU D 162 REMARK 465 ASN D 163 REMARK 465 LYS D 164 REMARK 465 ARG E 16 REMARK 465 LYS E 17 REMARK 465 GLU E 18 REMARK 465 ASN E 19 REMARK 465 ILE E 20 REMARK 465 GLY E 21 REMARK 465 GLU E 22 REMARK 465 ASN E 23 REMARK 465 GLU E 24 REMARK 465 LYS E 25 REMARK 465 GLU E 26 REMARK 465 LEU E 27 REMARK 465 ILE E 160 REMARK 465 ASN E 161 REMARK 465 LEU E 162 REMARK 465 ASN E 163 REMARK 465 LYS E 164 REMARK 465 LYS F 17 REMARK 465 GLU F 18 REMARK 465 ASN F 19 REMARK 465 ILE F 20 REMARK 465 GLY F 21 REMARK 465 GLU F 22 REMARK 465 ASN F 23 REMARK 465 GLU F 24 REMARK 465 LYS F 25 REMARK 465 ASN F 161 REMARK 465 LEU F 162 REMARK 465 ASN F 163 REMARK 465 LYS F 164 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 MET A 1 CG SD CE REMARK 470 GLU A 26 CG CD OE1 OE2 REMARK 470 LYS A 45 CG CD CE NZ REMARK 470 LYS A 70 CG CD CE NZ REMARK 470 LYS A 77 CG CD CE NZ REMARK 470 LYS A 97 CG CD CE NZ REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 ILE A 160 CG1 CG2 CD1 REMARK 470 MET B 1 CG SD CE REMARK 470 LYS B 17 CG CD CE NZ REMARK 470 GLU B 18 CG CD OE1 OE2 REMARK 470 ASN B 23 CG OD1 ND2 REMARK 470 GLU B 24 CG CD OE1 OE2 REMARK 470 LYS B 25 CG CD CE NZ REMARK 470 LYS B 45 CG CD CE NZ REMARK 470 LYS B 70 CG CD CE NZ REMARK 470 LYS B 96 CG CD CE NZ REMARK 470 LYS B 97 CG CD CE NZ REMARK 470 LYS B 100 CG CD CE NZ REMARK 470 LYS B 118 CG CD CE NZ REMARK 470 ILE B 160 CG1 CG2 CD1 REMARK 470 MET C 1 CG SD CE REMARK 470 LYS C 17 CG CD CE NZ REMARK 470 GLU C 18 CG CD OE1 OE2 REMARK 470 ASN C 23 CG OD1 ND2 REMARK 470 GLU C 24 CG CD OE1 OE2 REMARK 470 LYS C 25 CG CD CE NZ REMARK 470 GLU C 26 CG CD OE1 OE2 REMARK 470 LYS C 45 CG CD CE NZ REMARK 470 LYS C 58 CG CD CE NZ REMARK 470 ASP C 68 CG OD1 OD2 REMARK 470 ASN C 69 CG OD1 ND2 REMARK 470 LYS C 70 CG CD CE NZ REMARK 470 LYS C 74 CG CD CE NZ REMARK 470 LYS C 77 CG CD CE NZ REMARK 470 LYS C 97 CG CD CE NZ REMARK 470 LYS C 100 CG CD CE NZ REMARK 470 ASP C 102 CG OD1 OD2 REMARK 470 LYS C 107 CG CD CE NZ REMARK 470 GLU C 108 CG CD OE1 OE2 REMARK 470 LYS C 133 CG CD CE NZ REMARK 470 LYS C 136 CG CD CE NZ REMARK 470 ASP C 159 CG OD1 OD2 REMARK 470 MET D 1 CG SD CE REMARK 470 LYS D 17 CG CD CE NZ REMARK 470 LYS D 45 CG CD CE NZ REMARK 470 ARG D 57 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 70 CG CD CE NZ REMARK 470 LYS D 74 CG CD CE NZ REMARK 470 LYS D 77 CG CD CE NZ REMARK 470 LYS D 96 CG CD CE NZ REMARK 470 LYS D 97 CG CD CE NZ REMARK 470 LYS D 133 CG CD CE NZ REMARK 470 LYS D 136 CG CD CE NZ REMARK 470 MET E 1 CG SD CE REMARK 470 LYS E 9 CG CD CE NZ REMARK 470 LYS E 34 CG CD CE NZ REMARK 470 LYS E 45 CG CD CE NZ REMARK 470 LYS E 70 CG CD CE NZ REMARK 470 LYS E 97 CG CD CE NZ REMARK 470 LYS E 118 CG CD CE NZ REMARK 470 LYS E 125 CG CD CE NZ REMARK 470 LYS E 136 CG CD CE NZ REMARK 470 MET F 1 CG SD CE REMARK 470 GLU F 26 CG CD OE1 OE2 REMARK 470 LYS F 45 CG CD CE NZ REMARK 470 ASN F 69 CG OD1 ND2 REMARK 470 LYS F 96 CG CD CE NZ REMARK 470 LYS F 97 CG CD CE NZ REMARK 470 LYS F 100 CG CD CE NZ REMARK 470 LYS F 118 CG CD CE NZ REMARK 470 LYS F 125 CG CD CE NZ REMARK 470 ASP F 129 CG OD1 OD2 REMARK 470 LYS F 133 CG CD CE NZ 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 OD1 ASP A 148 OH TYR B 140 2.08 REMARK 500 OH TYR A 140 OD1 ASP B 148 2.19 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 41 CA - CB - CG ANGL. DEV. = 16.6 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 GLU A 28 116.45 -167.89 REMARK 500 LYS A 34 -146.26 -73.71 REMARK 500 ASN A 67 77.04 -117.93 REMARK 500 ASP A 68 84.85 15.89 REMARK 500 ASN A 69 -39.04 109.68 REMARK 500 ASP A 73 -31.45 -134.49 REMARK 500 ASP A 78 -37.85 -36.83 REMARK 500 ASN A 80 54.82 24.13 REMARK 500 LYS A 97 -88.93 -42.37 REMARK 500 LYS A 125 -38.82 -33.21 REMARK 500 TYR A 127 -85.81 -96.97 REMARK 500 ASP A 159 -28.18 -144.64 REMARK 500 ALA B 11 137.58 -173.23 REMARK 500 GLU B 24 -87.93 -125.94 REMARK 500 LYS B 25 47.99 22.68 REMARK 500 LYS B 34 -134.38 -84.60 REMARK 500 LYS B 45 -66.51 -22.60 REMARK 500 ASN B 46 49.79 -104.34 REMARK 500 ARG B 63 71.61 -100.88 REMARK 500 ASP B 68 -113.42 33.88 REMARK 500 TRP B 72 47.40 35.65 REMARK 500 THR B 90 8.37 -54.64 REMARK 500 TYR B 127 -128.72 -134.11 REMARK 500 ASP B 148 77.29 -106.97 REMARK 500 HIS B 158 23.61 -68.71 REMARK 500 GLU C 24 -135.46 -51.52 REMARK 500 LYS C 25 -97.54 -89.07 REMARK 500 GLU C 26 -66.90 145.23 REMARK 500 LYS C 34 -126.32 -93.00 REMARK 500 TRP C 49 -17.49 -49.26 REMARK 500 ILE C 55 -73.30 -39.71 REMARK 500 LEU C 64 -33.54 -130.10 REMARK 500 ASP C 68 96.12 -39.83 REMARK 500 ASN C 69 -70.81 119.13 REMARK 500 TRP C 72 35.18 39.27 REMARK 500 LYS C 96 -36.82 -38.93 REMARK 500 LYS C 97 -78.92 -42.64 REMARK 500 TYR C 127 -93.20 -137.69 REMARK 500 PHE C 137 -79.49 -41.80 REMARK 500 HIS C 158 15.52 -66.88 REMARK 500 SER D 31 144.24 -175.95 REMARK 500 LYS D 34 -132.35 -84.60 REMARK 500 CYS D 39 57.81 -112.70 REMARK 500 PHE D 40 111.91 -35.97 REMARK 500 ASP D 51 -73.76 -41.11 REMARK 500 ASP D 68 -117.28 46.25 REMARK 500 TRP D 72 74.36 31.82 REMARK 500 ASN D 99 39.70 -77.36 REMARK 500 LEU D 105 -0.21 -55.04 REMARK 500 LYS D 107 138.94 -36.14 REMARK 500 REMARK 500 THIS ENTRY HAS 84 RAMACHANDRAN OUTLIERS. 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 DSN B 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSN C 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSN D 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DSN D 166 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KNF RELATED DB: PDB REMARK 900 RELATED ID: 3KNP RELATED DB: PDB REMARK 900 RELATED ID: 3KO3 RELATED DB: PDB REMARK 900 RELATED ID: 3KO4 RELATED DB: PDB REMARK 900 RELATED ID: 3KO5 RELATED DB: PDB REMARK 900 RELATED ID: 3KO7 RELATED DB: PDB REMARK 900 RELATED ID: 3KO9 RELATED DB: PDB REMARK 900 RELATED ID: 3KOB RELATED DB: PDB REMARK 900 RELATED ID: 3KOC RELATED DB: PDB DBREF 3KOD A 1 164 UNP Q8IIS0 Q8IIS0_PLAF7 1 164 DBREF 3KOD B 1 164 UNP Q8IIS0 Q8IIS0_PLAF7 1 164 DBREF 3KOD C 1 164 UNP Q8IIS0 Q8IIS0_PLAF7 1 164 DBREF 3KOD D 1 164 UNP Q8IIS0 Q8IIS0_PLAF7 1 164 DBREF 3KOD E 1 164 UNP Q8IIS0 Q8IIS0_PLAF7 1 164 DBREF 3KOD F 1 164 UNP Q8IIS0 Q8IIS0_PLAF7 1 164 SEQRES 1 A 164 MET ARG VAL VAL ILE GLN ARG VAL LYS GLY ALA ILE LEU SEQRES 2 A 164 SER VAL ARG LYS GLU ASN ILE GLY GLU ASN GLU LYS GLU SEQRES 3 A 164 LEU GLU ILE ILE SER GLU ILE LYS ASN GLY LEU ILE CYS SEQRES 4 A 164 PHE LEU GLY ILE HIS LYS ASN ASP THR TRP GLU ASP ALA SEQRES 5 A 164 LEU TYR ILE ILE ARG LYS CYS LEU ASN LEU ARG LEU TRP SEQRES 6 A 164 ASN ASN ASP ASN LYS THR TRP ASP LYS ASN VAL LYS ASP SEQRES 7 A 164 LEU ASN TYR GLU LEU LEU ILE VAL SER GLN PHE THR LEU SEQRES 8 A 164 PHE GLY ASN THR LYS LYS GLY ASN LYS PRO ASP PHE HIS SEQRES 9 A 164 LEU ALA LYS GLU PRO ASN GLU ALA LEU ILE PHE TYR ASN SEQRES 10 A 164 LYS ILE ILE ASP GLU PHE LYS LYS GLN TYR ASN ASP ASP SEQRES 11 A 164 LYS ILE LYS ILE GLY LYS PHE GLY ASN TYR MET ASN ILE SEQRES 12 A 164 ASP VAL THR ASN ASP GLY PRO VAL THR ILE TYR ILE ASP SEQRES 13 A 164 THR HIS ASP ILE ASN LEU ASN LYS SEQRES 1 B 164 MET ARG VAL VAL ILE GLN ARG VAL LYS GLY ALA ILE LEU SEQRES 2 B 164 SER VAL ARG LYS GLU ASN ILE GLY GLU ASN GLU LYS GLU SEQRES 3 B 164 LEU GLU ILE ILE SER GLU ILE LYS ASN GLY LEU ILE CYS SEQRES 4 B 164 PHE LEU GLY ILE HIS LYS ASN ASP THR TRP GLU ASP ALA SEQRES 5 B 164 LEU TYR ILE ILE ARG LYS CYS LEU ASN LEU ARG LEU TRP SEQRES 6 B 164 ASN ASN ASP ASN LYS THR TRP ASP LYS ASN VAL LYS ASP SEQRES 7 B 164 LEU ASN TYR GLU LEU LEU ILE VAL SER GLN PHE THR LEU SEQRES 8 B 164 PHE GLY ASN THR LYS LYS GLY ASN LYS PRO ASP PHE HIS SEQRES 9 B 164 LEU ALA LYS GLU PRO ASN GLU ALA LEU ILE PHE TYR ASN SEQRES 10 B 164 LYS ILE ILE ASP GLU PHE LYS LYS GLN TYR ASN ASP ASP SEQRES 11 B 164 LYS ILE LYS ILE GLY LYS PHE GLY ASN TYR MET ASN ILE SEQRES 12 B 164 ASP VAL THR ASN ASP GLY PRO VAL THR ILE TYR ILE ASP SEQRES 13 B 164 THR HIS ASP ILE ASN LEU ASN LYS SEQRES 1 C 164 MET ARG VAL VAL ILE GLN ARG VAL LYS GLY ALA ILE LEU SEQRES 2 C 164 SER VAL ARG LYS GLU ASN ILE GLY GLU ASN GLU LYS GLU SEQRES 3 C 164 LEU GLU ILE ILE SER GLU ILE LYS ASN GLY LEU ILE CYS SEQRES 4 C 164 PHE LEU GLY ILE HIS LYS ASN ASP THR TRP GLU ASP ALA SEQRES 5 C 164 LEU TYR ILE ILE ARG LYS CYS LEU ASN LEU ARG LEU TRP SEQRES 6 C 164 ASN ASN ASP ASN LYS THR TRP ASP LYS ASN VAL LYS ASP SEQRES 7 C 164 LEU ASN TYR GLU LEU LEU ILE VAL SER GLN PHE THR LEU SEQRES 8 C 164 PHE GLY ASN THR LYS LYS GLY ASN LYS PRO ASP PHE HIS SEQRES 9 C 164 LEU ALA LYS GLU PRO ASN GLU ALA LEU ILE PHE TYR ASN SEQRES 10 C 164 LYS ILE ILE ASP GLU PHE LYS LYS GLN TYR ASN ASP ASP SEQRES 11 C 164 LYS ILE LYS ILE GLY LYS PHE GLY ASN TYR MET ASN ILE SEQRES 12 C 164 ASP VAL THR ASN ASP GLY PRO VAL THR ILE TYR ILE ASP SEQRES 13 C 164 THR HIS ASP ILE ASN LEU ASN LYS SEQRES 1 D 164 MET ARG VAL VAL ILE GLN ARG VAL LYS GLY ALA ILE LEU SEQRES 2 D 164 SER VAL ARG LYS GLU ASN ILE GLY GLU ASN GLU LYS GLU SEQRES 3 D 164 LEU GLU ILE ILE SER GLU ILE LYS ASN GLY LEU ILE CYS SEQRES 4 D 164 PHE LEU GLY ILE HIS LYS ASN ASP THR TRP GLU ASP ALA SEQRES 5 D 164 LEU TYR ILE ILE ARG LYS CYS LEU ASN LEU ARG LEU TRP SEQRES 6 D 164 ASN ASN ASP ASN LYS THR TRP ASP LYS ASN VAL LYS ASP SEQRES 7 D 164 LEU ASN TYR GLU LEU LEU ILE VAL SER GLN PHE THR LEU SEQRES 8 D 164 PHE GLY ASN THR LYS LYS GLY ASN LYS PRO ASP PHE HIS SEQRES 9 D 164 LEU ALA LYS GLU PRO ASN GLU ALA LEU ILE PHE TYR ASN SEQRES 10 D 164 LYS ILE ILE ASP GLU PHE LYS LYS GLN TYR ASN ASP ASP SEQRES 11 D 164 LYS ILE LYS ILE GLY LYS PHE GLY ASN TYR MET ASN ILE SEQRES 12 D 164 ASP VAL THR ASN ASP GLY PRO VAL THR ILE TYR ILE ASP SEQRES 13 D 164 THR HIS ASP ILE ASN LEU ASN LYS SEQRES 1 E 164 MET ARG VAL VAL ILE GLN ARG VAL LYS GLY ALA ILE LEU SEQRES 2 E 164 SER VAL ARG LYS GLU ASN ILE GLY GLU ASN GLU LYS GLU SEQRES 3 E 164 LEU GLU ILE ILE SER GLU ILE LYS ASN GLY LEU ILE CYS SEQRES 4 E 164 PHE LEU GLY ILE HIS LYS ASN ASP THR TRP GLU ASP ALA SEQRES 5 E 164 LEU TYR ILE ILE ARG LYS CYS LEU ASN LEU ARG LEU TRP SEQRES 6 E 164 ASN ASN ASP ASN LYS THR TRP ASP LYS ASN VAL LYS ASP SEQRES 7 E 164 LEU ASN TYR GLU LEU LEU ILE VAL SER GLN PHE THR LEU SEQRES 8 E 164 PHE GLY ASN THR LYS LYS GLY ASN LYS PRO ASP PHE HIS SEQRES 9 E 164 LEU ALA LYS GLU PRO ASN GLU ALA LEU ILE PHE TYR ASN SEQRES 10 E 164 LYS ILE ILE ASP GLU PHE LYS LYS GLN TYR ASN ASP ASP SEQRES 11 E 164 LYS ILE LYS ILE GLY LYS PHE GLY ASN TYR MET ASN ILE SEQRES 12 E 164 ASP VAL THR ASN ASP GLY PRO VAL THR ILE TYR ILE ASP SEQRES 13 E 164 THR HIS ASP ILE ASN LEU ASN LYS SEQRES 1 F 164 MET ARG VAL VAL ILE GLN ARG VAL LYS GLY ALA ILE LEU SEQRES 2 F 164 SER VAL ARG LYS GLU ASN ILE GLY GLU ASN GLU LYS GLU SEQRES 3 F 164 LEU GLU ILE ILE SER GLU ILE LYS ASN GLY LEU ILE CYS SEQRES 4 F 164 PHE LEU GLY ILE HIS LYS ASN ASP THR TRP GLU ASP ALA SEQRES 5 F 164 LEU TYR ILE ILE ARG LYS CYS LEU ASN LEU ARG LEU TRP SEQRES 6 F 164 ASN ASN ASP ASN LYS THR TRP ASP LYS ASN VAL LYS ASP SEQRES 7 F 164 LEU ASN TYR GLU LEU LEU ILE VAL SER GLN PHE THR LEU SEQRES 8 F 164 PHE GLY ASN THR LYS LYS GLY ASN LYS PRO ASP PHE HIS SEQRES 9 F 164 LEU ALA LYS GLU PRO ASN GLU ALA LEU ILE PHE TYR ASN SEQRES 10 F 164 LYS ILE ILE ASP GLU PHE LYS LYS GLN TYR ASN ASP ASP SEQRES 11 F 164 LYS ILE LYS ILE GLY LYS PHE GLY ASN TYR MET ASN ILE SEQRES 12 F 164 ASP VAL THR ASN ASP GLY PRO VAL THR ILE TYR ILE ASP SEQRES 13 F 164 THR HIS ASP ILE ASN LEU ASN LYS HET DSN B 165 7 HET DSN C 165 7 HET DSN D 165 7 HET DSN D 166 7 HETNAM DSN D-SERINE FORMUL 7 DSN 4(C3 H7 N O3) HELIX 1 1 THR A 48 LEU A 62 1 15 HELIX 2 2 GLN A 88 GLY A 93 5 6 HELIX 3 3 GLU A 108 TYR A 127 1 20 HELIX 4 4 THR B 48 LEU B 62 1 15 HELIX 5 5 PHE B 89 PHE B 92 5 4 HELIX 6 6 GLU B 108 GLN B 126 1 19 HELIX 7 7 ASN B 128 ASP B 130 5 3 HELIX 8 8 HIS B 158 ILE B 160 5 3 HELIX 9 9 THR C 48 LEU C 62 1 15 HELIX 10 10 VAL C 76 ASN C 80 1 5 HELIX 11 11 PHE C 89 GLY C 93 5 5 HELIX 12 12 GLU C 108 LYS C 125 1 18 HELIX 13 13 GLN C 126 TYR C 127 5 2 HELIX 14 14 ASN C 128 ASP C 130 5 3 HELIX 15 15 THR D 48 LEU D 62 1 15 HELIX 16 16 LYS D 77 ASN D 80 5 4 HELIX 17 17 GLN D 88 PHE D 92 5 5 HELIX 18 18 GLU D 108 TYR D 127 1 20 HELIX 19 19 THR E 48 LEU E 62 1 15 HELIX 20 20 LYS E 77 ASN E 80 5 4 HELIX 21 21 PHE E 89 GLY E 93 5 5 HELIX 22 22 ASN E 110 TYR E 127 1 18 HELIX 23 23 ASN E 128 ILE E 132 5 5 HELIX 24 24 THR F 48 LEU F 62 1 15 HELIX 25 25 PHE F 89 GLY F 93 5 5 HELIX 26 26 ASN F 110 TYR F 127 1 18 CISPEP 1 GLY A 149 PRO A 150 0 8.19 CISPEP 2 GLY B 149 PRO B 150 0 -3.67 CISPEP 3 GLY C 149 PRO C 150 0 -4.24 CISPEP 4 GLY D 149 PRO D 150 0 -2.87 CISPEP 5 GLY E 149 PRO E 150 0 5.03 CISPEP 6 GLY F 149 PRO F 150 0 -0.84 SITE 1 AC1 4 ARG B 7 ASN B 66 THR B 71 TRP B 72 SITE 1 AC2 2 TRP C 72 TYR D 140 SITE 1 AC3 3 PHE D 89 PRO D 109 GLY D 138 SITE 1 AC4 2 ASN C 66 ARG D 16 CRYST1 52.281 55.147 92.535 106.86 101.86 94.45 P 1 6 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 0.019127 0.001488 0.004722 0.00000 SCALE2 0.000000 0.018188 0.006008 0.00000 SCALE3 0.000000 0.000000 0.011629 0.00000