HEADER HYDROLASE 18-FEB-11 3QRV TITLE CRYSTAL STRUCTURE OF PLASMEPSIN I (PMI) FROM PLASMODIUM FALCIPARUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PLASMEPSIN-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 117-452; COMPND 5 SYNONYM: ASPARTIC HEMOGLOBINASE I, PFAPG; COMPND 6 EC: 3.4.23.38; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 5833; SOURCE 4 GENE: PMI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ROSETTA-GAMI B (DE3) PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET32B(+) KEYWDS ASPARTIC PROTEASE, MALARIA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.BHAUMIK,A.GUSTCHINA,A.WLODAWER REVDAT 2 22-JUN-11 3QRV 1 JRNL REVDAT 1 11-MAY-11 3QRV 0 JRNL AUTH P.BHAUMIK,Y.HORIMOTO,H.XIAO,T.MIURA,K.HIDAKA,Y.KISO, JRNL AUTH 2 A.WLODAWER,R.Y.YADA,A.GUSTCHINA JRNL TITL CRYSTAL STRUCTURES OF THE FREE AND INHIBITED FORMS OF JRNL TITL 2 PLASMEPSIN I (PMI) FROM PLASMODIUM FALCIPARUM. JRNL REF J.STRUCT.BIOL. V. 175 73 2011 JRNL REFN ISSN 1047-8477 JRNL PMID 21521654 JRNL DOI 10.1016/J.JSB.2011.04.009 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0104 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 27830 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) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1465 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1983 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE SET COUNT : 105 REMARK 3 BIN FREE R VALUE : 0.3980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5191 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.65000 REMARK 3 B22 (A**2) : 1.36000 REMARK 3 B33 (A**2) : 2.29000 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): 0.304 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.253 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 24.830 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.942 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): 5325 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7235 ; 2.186 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 649 ; 8.603 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 249 ;37.569 ;25.462 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 874 ;22.079 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;20.794 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 805 ; 0.158 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4050 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 3235 ; 0.982 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5254 ; 1.727 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2090 ; 2.510 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1981 ; 3.789 ; 4.500 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 190 REMARK 3 ORIGIN FOR THE GROUP (A): 29.9660 20.2810 38.1400 REMARK 3 T TENSOR REMARK 3 T11: 0.4937 T22: 0.0942 REMARK 3 T33: 0.1763 T12: -0.0740 REMARK 3 T13: -0.0665 T23: -0.0111 REMARK 3 L TENSOR REMARK 3 L11: 1.9649 L22: 5.5305 REMARK 3 L33: 2.4311 L12: 0.4541 REMARK 3 L13: -0.5109 L23: 1.2716 REMARK 3 S TENSOR REMARK 3 S11: 0.0741 S12: -0.1339 S13: 0.2370 REMARK 3 S21: 0.3917 S22: -0.1831 S23: 0.4865 REMARK 3 S31: -0.1161 S32: -0.0116 S33: 0.1090 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 191 A 328 REMARK 3 ORIGIN FOR THE GROUP (A): 27.0850 5.7980 19.1830 REMARK 3 T TENSOR REMARK 3 T11: 0.4787 T22: 0.0273 REMARK 3 T33: 0.1143 T12: 0.0099 REMARK 3 T13: 0.0296 T23: 0.0290 REMARK 3 L TENSOR REMARK 3 L11: 2.2407 L22: 1.7668 REMARK 3 L33: 1.7448 L12: 0.8697 REMARK 3 L13: 0.9513 L23: 0.0351 REMARK 3 S TENSOR REMARK 3 S11: 0.0256 S12: -0.1611 S13: -0.1274 REMARK 3 S21: -0.0239 S22: 0.0194 S23: -0.0199 REMARK 3 S31: 0.0953 S32: -0.0251 S33: -0.0450 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 0 B 190 REMARK 3 ORIGIN FOR THE GROUP (A): 0.4070 36.3030 9.7700 REMARK 3 T TENSOR REMARK 3 T11: 0.5460 T22: 0.0636 REMARK 3 T33: 0.1136 T12: 0.0597 REMARK 3 T13: -0.0273 T23: -0.0208 REMARK 3 L TENSOR REMARK 3 L11: 4.1209 L22: 1.9257 REMARK 3 L33: 1.3663 L12: 1.0528 REMARK 3 L13: 0.3609 L23: 0.0727 REMARK 3 S TENSOR REMARK 3 S11: -0.0096 S12: -0.2819 S13: -0.1016 REMARK 3 S21: 0.1008 S22: 0.0505 S23: -0.2657 REMARK 3 S31: -0.0802 S32: 0.1615 S33: -0.0409 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 191 B 328 REMARK 3 ORIGIN FOR THE GROUP (A): -8.0590 17.0940 21.3390 REMARK 3 T TENSOR REMARK 3 T11: 0.4746 T22: 0.1409 REMARK 3 T33: 0.1576 T12: -0.0413 REMARK 3 T13: -0.0105 T23: 0.0669 REMARK 3 L TENSOR REMARK 3 L11: 3.0189 L22: 3.3288 REMARK 3 L33: 1.8103 L12: -2.3108 REMARK 3 L13: 1.0499 L23: -0.9603 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.3132 S13: -0.1651 REMARK 3 S21: 0.1519 S22: 0.1110 S23: 0.1368 REMARK 3 S31: -0.0353 S32: -0.2261 S33: -0.1070 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: NULL REMARK 4 REMARK 4 3QRV COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-11. REMARK 100 THE RCSB ID CODE IS RCSB064024. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 : NULL 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29306 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.20500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.50 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 7.20 REMARK 200 R MERGE FOR SHELL (I) : 0.13130 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 6000, 0.1M SODIUM ACETATE, PH REMARK 280 4.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 36.08500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 54.43500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 46.69500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 54.43500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.08500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 46.69500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 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 THR A -8 REMARK 465 GLN A -7 REMARK 465 LYS A -6 REMARK 465 PRO A -5 REMARK 465 HIS A -4 REMARK 465 LEU A -3 REMARK 465 GLY A -2 REMARK 465 ASN A -1 REMARK 465 MET A 73 REMARK 465 ASN A 74 REMARK 465 TYR A 75 REMARK 465 VAL A 76 REMARK 465 SER A 77 REMARK 465 THR B -8 REMARK 465 GLN B -7 REMARK 465 LYS B -6 REMARK 465 PRO B -5 REMARK 465 HIS B -4 REMARK 465 LEU B -3 REMARK 465 GLY B -2 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 A 332 O HOH A 409 2.00 REMARK 500 N GLY A 49 O HOH A 341 2.12 REMARK 500 CG ASN B 250 O HOH B 358 2.17 REMARK 500 OG SER B 35 O HOH B 406 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 14 CE2 TYR A 14 CD2 0.098 REMARK 500 TYR A 245 CD1 TYR A 245 CE1 0.096 REMARK 500 VAL A 284 CB VAL A 284 CG1 -0.152 REMARK 500 GLU B 147 CD GLU B 147 OE1 0.066 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 VAL A 320 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 ASP B 32 CB - CG - OD2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP B 172 CB - CG - OD1 ANGL. DEV. = 6.6 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 ASN A 11 5.19 83.45 REMARK 500 ASN A 23 8.39 -61.52 REMARK 500 LYS A 24 68.76 37.59 REMARK 500 ALA A 36 15.39 -146.00 REMARK 500 GLN A 44 32.53 -96.01 REMARK 500 THR A 79 28.21 123.50 REMARK 500 ASP A 87 171.03 178.89 REMARK 500 ASN A 93 19.77 38.94 REMARK 500 ALA A 111 63.64 -169.07 REMARK 500 GLN A 116 50.14 -96.03 REMARK 500 SER A 132 70.01 44.32 REMARK 500 GLU A 139 -59.30 -29.14 REMARK 500 ARG A 173 -17.21 -41.38 REMARK 500 LEU A 188 -92.95 -161.54 REMARK 500 PHE A 242 -1.72 77.98 REMARK 500 ASN A 250 56.78 -95.40 REMARK 500 ASP A 279 -1.13 -150.37 REMARK 500 SER A 285 39.62 -85.45 REMARK 500 LEU A 291 -159.50 -100.32 REMARK 500 ASN A 292 158.05 -44.20 REMARK 500 ASP A 303 -34.76 -38.06 REMARK 500 HIS A 318 51.04 35.43 REMARK 500 ALA B 10 21.12 40.71 REMARK 500 ASN B 11 27.25 80.15 REMARK 500 THR B 47 159.82 -30.78 REMARK 500 ASP B 67 -65.76 -139.08 REMARK 500 ALA B 92 -120.02 56.30 REMARK 500 PHE B 157 -33.42 -37.38 REMARK 500 ASP B 158 -158.32 -158.38 REMARK 500 PHE B 242 3.69 58.69 REMARK 500 PRO B 243A 57.62 -69.40 REMARK 500 ASP B 279 46.38 -153.20 REMARK 500 LEU B 291 -145.65 -110.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 109B PRO A 110 136.72 REMARK 500 ILE B 130 GLY B 131 -41.43 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 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE 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: (10X,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 THR A 79 23.4 L L OUTSIDE RANGE REMARK 500 ASN A 93 25.0 L L OUTSIDE RANGE REMARK 500 LYS A 296 23.9 L L OUTSIDE RANGE REMARK 500 VAL B 9 23.4 L L OUTSIDE RANGE REMARK 500 SER B 77 22.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3QS1 RELATED DB: PDB REMARK 900 RELATED ID: 3QVC RELATED DB: PDB REMARK 900 RELATED ID: 3QVI RELATED DB: PDB DBREF 3QRV A -8 329 UNP P39898 PLM1_PLAFA 117 452 DBREF 3QRV B -8 329 UNP P39898 PLM1_PLAFA 117 452 SEQRES 1 A 336 THR GLN LYS PRO HIS LEU GLY ASN ALA GLY ASP SER VAL SEQRES 2 A 336 THR LEU ASN ASP VAL ALA ASN VAL MET TYR TYR GLY GLU SEQRES 3 A 336 ALA GLN ILE GLY ASP ASN LYS GLN LYS PHE ALA PHE ILE SEQRES 4 A 336 PHE ASP THR GLY SER ALA ASN LEU TRP VAL PRO SER ALA SEQRES 5 A 336 GLN CYS ASN THR ILE GLY CYS LYS THR LYS ASN LEU TYR SEQRES 6 A 336 ASP SER ASN LYS SER LYS THR TYR GLU LYS ASP GLY THR SEQRES 7 A 336 LYS VAL GLU MET ASN TYR VAL SER GLY THR VAL SER GLY SEQRES 8 A 336 PHE PHE SER LYS ASP ILE VAL THR ILE ALA ASN LEU SER SEQRES 9 A 336 PHE PRO TYR LYS PHE ILE GLU VAL THR ASP THR ASN GLY SEQRES 10 A 336 PHE GLU PRO ALA TYR THR LEU GLY GLN PHE ASP GLY ILE SEQRES 11 A 336 VAL GLY LEU GLY TRP LYS ASP LEU SER ILE GLY SER VAL SEQRES 12 A 336 ASP PRO VAL VAL VAL GLU LEU LYS ASN GLN ASN LYS ILE SEQRES 13 A 336 GLU GLN ALA VAL PHE THR PHE TYR LEU PRO PHE ASP ASP SEQRES 14 A 336 LYS HIS LYS GLY TYR LEU THR ILE GLY GLY ILE GLU ASP SEQRES 15 A 336 ARG PHE TYR GLU GLY GLN LEU THR TYR GLU LYS LEU ASN SEQRES 16 A 336 HIS ASP LEU TYR TRP GLN VAL ASP LEU ASP LEU HIS PHE SEQRES 17 A 336 GLY ASN LEU THR VAL GLU LYS ALA THR ALA ILE VAL ASP SEQRES 18 A 336 SER GLY THR SER SER ILE THR ALA PRO THR GLU PHE LEU SEQRES 19 A 336 ASN LYS PHE PHE GLU GLY LEU ASP VAL VAL LYS ILE PRO SEQRES 20 A 336 PHE LEU PRO LEU TYR ILE THR THR CYS ASN ASN PRO LYS SEQRES 21 A 336 LEU PRO THR LEU GLU PHE ARG SER ALA THR ASN VAL TYR SEQRES 22 A 336 THR LEU GLU PRO GLU TYR TYR LEU GLN GLN ILE PHE ASP SEQRES 23 A 336 PHE GLY ILE SER LEU CYS MET VAL SER ILE ILE PRO VAL SEQRES 24 A 336 ASP LEU ASN LYS ASN THR PHE ILE LEU GLY ASP PRO PHE SEQRES 25 A 336 MET ARG LYS TYR PHE THR VAL PHE ASP TYR ASP ASN HIS SEQRES 26 A 336 THR VAL GLY PHE ALA LEU ALA LYS LYS LYS LEU SEQRES 1 B 336 THR GLN LYS PRO HIS LEU GLY ASN ALA GLY ASP SER VAL SEQRES 2 B 336 THR LEU ASN ASP VAL ALA ASN VAL MET TYR TYR GLY GLU SEQRES 3 B 336 ALA GLN ILE GLY ASP ASN LYS GLN LYS PHE ALA PHE ILE SEQRES 4 B 336 PHE ASP THR GLY SER ALA ASN LEU TRP VAL PRO SER ALA SEQRES 5 B 336 GLN CYS ASN THR ILE GLY CYS LYS THR LYS ASN LEU TYR SEQRES 6 B 336 ASP SER ASN LYS SER LYS THR TYR GLU LYS ASP GLY THR SEQRES 7 B 336 LYS VAL GLU MET ASN TYR VAL SER GLY THR VAL SER GLY SEQRES 8 B 336 PHE PHE SER LYS ASP ILE VAL THR ILE ALA ASN LEU SER SEQRES 9 B 336 PHE PRO TYR LYS PHE ILE GLU VAL THR ASP THR ASN GLY SEQRES 10 B 336 PHE GLU PRO ALA TYR THR LEU GLY GLN PHE ASP GLY ILE SEQRES 11 B 336 VAL GLY LEU GLY TRP LYS ASP LEU SER ILE GLY SER VAL SEQRES 12 B 336 ASP PRO VAL VAL VAL GLU LEU LYS ASN GLN ASN LYS ILE SEQRES 13 B 336 GLU GLN ALA VAL PHE THR PHE TYR LEU PRO PHE ASP ASP SEQRES 14 B 336 LYS HIS LYS GLY TYR LEU THR ILE GLY GLY ILE GLU ASP SEQRES 15 B 336 ARG PHE TYR GLU GLY GLN LEU THR TYR GLU LYS LEU ASN SEQRES 16 B 336 HIS ASP LEU TYR TRP GLN VAL ASP LEU ASP LEU HIS PHE SEQRES 17 B 336 GLY ASN LEU THR VAL GLU LYS ALA THR ALA ILE VAL ASP SEQRES 18 B 336 SER GLY THR SER SER ILE THR ALA PRO THR GLU PHE LEU SEQRES 19 B 336 ASN LYS PHE PHE GLU GLY LEU ASP VAL VAL LYS ILE PRO SEQRES 20 B 336 PHE LEU PRO LEU TYR ILE THR THR CYS ASN ASN PRO LYS SEQRES 21 B 336 LEU PRO THR LEU GLU PHE ARG SER ALA THR ASN VAL TYR SEQRES 22 B 336 THR LEU GLU PRO GLU TYR TYR LEU GLN GLN ILE PHE ASP SEQRES 23 B 336 PHE GLY ILE SER LEU CYS MET VAL SER ILE ILE PRO VAL SEQRES 24 B 336 ASP LEU ASN LYS ASN THR PHE ILE LEU GLY ASP PRO PHE SEQRES 25 B 336 MET ARG LYS TYR PHE THR VAL PHE ASP TYR ASP ASN HIS SEQRES 26 B 336 THR VAL GLY PHE ALA LEU ALA LYS LYS LYS LEU FORMUL 3 HOH *188(H2 O) HELIX 1 1 GLY A 49 LYS A 53 5 5 HELIX 2 2 ASP A 57 SER A 61 5 5 HELIX 3 3 TRP A 125 SER A 129 5 5 HELIX 4 4 PRO A 135 GLN A 143 1 9 HELIX 5 5 GLU A 171 ARG A 173 5 3 HELIX 6 6 PRO A 224 GLU A 233 1 10 HELIX 7 7 GLU A 270 TYR A 274 1 5 HELIX 8 8 GLY A 302 LYS A 308 1 7 HELIX 9 9 ILE B 48 LYS B 53 5 6 HELIX 10 10 ASP B 57 SER B 61 5 5 HELIX 11 11 PRO B 110 GLY B 115 1 6 HELIX 12 12 PRO B 135 GLN B 143 1 9 HELIX 13 13 GLU B 171 TYR B 175 5 5 HELIX 14 14 PRO B 224 GLU B 233 1 10 HELIX 15 15 GLU B 270 TYR B 273 5 4 HELIX 16 16 GLY B 302 LYS B 308 1 7 SHEET 1 A 9 GLU A 65 VAL A 71 0 SHEET 2 A 9 VAL A 80 ILE A 91 -1 O LYS A 86 N GLU A 65 SHEET 3 A 9 MET A 13 ILE A 20 -1 N GLN A 19 O THR A 90 SHEET 4 A 9 ASP A 2 VAL A 9 -1 N ASN A 7 O TYR A 15 SHEET 5 A 9 GLY A 163 ILE A 167 -1 O GLY A 163 N LEU A 6 SHEET 6 A 9 VAL A 150 TYR A 154 -1 N TYR A 154 O TYR A 164 SHEET 7 A 9 TYR A 309 ASP A 314 -1 O PHE A 313 N PHE A 151 SHEET 8 A 9 THR A 319 ALA A 325 -1 O ALA A 323 N PHE A 310 SHEET 9 A 9 TYR A 175 LYS A 183 -1 N GLU A 182 O VAL A 320 SHEET 1 B13 GLU A 65 VAL A 71 0 SHEET 2 B13 VAL A 80 ILE A 91 -1 O LYS A 86 N GLU A 65 SHEET 3 B13 LEU A 94 THR A 107 -1 O LEU A 94 N ILE A 91 SHEET 4 B13 LEU A 38 PRO A 41 1 N VAL A 40 O VAL A 104 SHEET 5 B13 GLY A 119 GLY A 122 -1 O ILE A 120 N TRP A 39 SHEET 6 B13 GLN A 25 ASP A 32 1 N ILE A 30 O VAL A 121 SHEET 7 B13 MET A 13 ILE A 20 -1 N GLY A 16 O PHE A 29 SHEET 8 B13 ASP A 2 VAL A 9 -1 N ASN A 7 O TYR A 15 SHEET 9 B13 GLY A 163 ILE A 167 -1 O GLY A 163 N LEU A 6 SHEET 10 B13 VAL A 150 TYR A 154 -1 N TYR A 154 O TYR A 164 SHEET 11 B13 TYR A 309 ASP A 314 -1 O PHE A 313 N PHE A 151 SHEET 12 B13 THR A 319 ALA A 325 -1 O ALA A 323 N PHE A 310 SHEET 13 B13 TYR A 175 LYS A 183 -1 N GLU A 182 O VAL A 320 SHEET 1 C 7 VAL A 266 LEU A 269 0 SHEET 2 C 7 LEU A 258 ARG A 261 -1 N PHE A 260 O TYR A 267 SHEET 3 C 7 GLN A 191 PHE A 199 -1 N ASP A 195 O ARG A 261 SHEET 4 C 7 LEU A 205 VAL A 214 -1 O LEU A 205 N PHE A 199 SHEET 5 C 7 THR A 298 LEU A 301 1 O LEU A 301 N ILE A 213 SHEET 6 C 7 ILE A 221 ALA A 223 -1 N THR A 222 O ILE A 300 SHEET 7 C 7 ILE A 286 PRO A 288 1 O ILE A 287 N ILE A 221 SHEET 1 D 4 VAL A 238 LYS A 239 0 SHEET 2 D 4 TYR A 245 THR A 248 -1 O ILE A 246 N VAL A 238 SHEET 3 D 4 LEU A 281 VAL A 284 -1 O CYS A 282 N THR A 247 SHEET 4 D 4 LEU A 275 PHE A 278A-1 N ILE A 278 O LEU A 281 SHEET 1 E 9 GLU B 65 ASN B 74 0 SHEET 2 E 9 THR B 79 ILE B 91 -1 O GLY B 82 N VAL B 71 SHEET 3 E 9 MET B 13 ILE B 20 -1 N GLN B 19 O THR B 90 SHEET 4 E 9 ASP B 2 VAL B 9 -1 N ASN B 7 O TYR B 15 SHEET 5 E 9 GLY B 163 ILE B 167 -1 O LEU B 165 N VAL B 4 SHEET 6 E 9 VAL B 150 TYR B 154 -1 N THR B 152 O THR B 166 SHEET 7 E 9 TYR B 309 ASP B 314 -1 O PHE B 313 N PHE B 151 SHEET 8 E 9 THR B 319 LEU B 324 -1 O GLY B 321 N VAL B 312 SHEET 9 E 9 THR B 180 LYS B 183 -1 N GLU B 182 O VAL B 320 SHEET 1 F13 GLU B 65 ASN B 74 0 SHEET 2 F13 THR B 79 ILE B 91 -1 O GLY B 82 N VAL B 71 SHEET 3 F13 LEU B 94 GLY B 109 -1 O GLU B 103 N PHE B 83 SHEET 4 F13 LEU B 38 PRO B 41 1 N VAL B 40 O VAL B 104 SHEET 5 F13 GLY B 119 GLY B 122 -1 O ILE B 120 N TRP B 39 SHEET 6 F13 GLN B 25 ASP B 32 1 N ILE B 30 O VAL B 121 SHEET 7 F13 MET B 13 ILE B 20 -1 N GLY B 16 O PHE B 29 SHEET 8 F13 ASP B 2 VAL B 9 -1 N ASN B 7 O TYR B 15 SHEET 9 F13 GLY B 163 ILE B 167 -1 O LEU B 165 N VAL B 4 SHEET 10 F13 VAL B 150 TYR B 154 -1 N THR B 152 O THR B 166 SHEET 11 F13 TYR B 309 ASP B 314 -1 O PHE B 313 N PHE B 151 SHEET 12 F13 THR B 319 LEU B 324 -1 O GLY B 321 N VAL B 312 SHEET 13 F13 THR B 180 LYS B 183 -1 N GLU B 182 O VAL B 320 SHEET 1 G 7 VAL B 266 LEU B 269 0 SHEET 2 G 7 LEU B 258 ARG B 261 -1 N PHE B 260 O TYR B 267 SHEET 3 G 7 GLN B 191 PHE B 199 -1 N ASP B 195 O ARG B 261 SHEET 4 G 7 LEU B 205 VAL B 214 -1 O ALA B 212 N VAL B 192 SHEET 5 G 7 THR B 298 LEU B 301 1 O LEU B 301 N ILE B 213 SHEET 6 G 7 ILE B 221 ALA B 223 -1 N THR B 222 O ILE B 300 SHEET 7 G 7 ILE B 286 PRO B 288 1 O ILE B 287 N ILE B 221 SHEET 1 H 4 VAL B 238 LYS B 239 0 SHEET 2 H 4 TYR B 245 THR B 248 -1 O ILE B 246 N VAL B 238 SHEET 3 H 4 LEU B 281 VAL B 284 -1 O VAL B 284 N TYR B 245 SHEET 4 H 4 LEU B 275 PHE B 278A-1 N ILE B 278 O LEU B 281 SSBOND 1 CYS A 45 CYS A 50 1555 1555 2.07 SSBOND 2 CYS A 249 CYS A 282 1555 1555 2.05 SSBOND 3 CYS B 45 CYS B 50 1555 1555 2.08 SSBOND 4 CYS B 249 CYS B 282 1555 1555 2.02 CISPEP 1 SER B 77 GLY B 78 0 7.60 CISPEP 2 GLU B 109B PRO B 110 0 -2.92 CRYST1 72.170 93.390 108.870 90.00 90.00 90.00 P 21 21 21 8 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 0.013856 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009185 0.00000