HEADER OXIDOREDUCTASE 12-FEB-15 4Y67 TITLE STRUCTURE OF PLASMODIUM FALCIPARUM DXR IN COMPLEX WITH A BETA- TITLE 2 SUBSTITUTED FOSMIDOMYCIN ANALOGUE, RC176, AND MANGANESE COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1-DEOXY-D-XYLULOSE 5-PHOSPHATE REDUCTOISOMERASE, COMPND 3 APICOPLAST; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: DXP REDUCTOISOMERASE; COMPND 6 EC: 1.1.1.267; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: MATURE PROTEIN LACKS SIGNAL AND APICOPLAST TARGETING COMPND 9 SEQUENCES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: 3D7; SOURCE 5 GENE: DXR, PF14_0641; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C43; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PEXP-5-CT/TOPO KEYWDS ENZYME-INHIBITOR COMPLEX, MEP PATHWAY, ISOPRENOID BIOSYNTHESIS, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SOORIYAARACHCHI,T.BERGFORS,T.A.JONES,S.L.MOWBRAY REVDAT 3 10-JAN-24 4Y67 1 LINK REVDAT 2 22-APR-15 4Y67 1 JRNL REVDAT 1 01-APR-15 4Y67 0 JRNL AUTH R.CHOFOR,S.SOORIYAARACHCHI,M.D.RISSEEUW,T.BERGFORS,J.POUYEZ, JRNL AUTH 2 C.JOHNY,A.HAYMOND,A.EVERAERT,C.S.DOWD,L.MAES,T.COENYE, JRNL AUTH 3 A.ALEX,R.D.COUCH,T.A.JONES,J.WOUTERS,S.L.MOWBRAY, JRNL AUTH 4 S.VAN CALENBERGH JRNL TITL SYNTHESIS AND BIOACTIVITY OF BETA-SUBSTITUTED FOSMIDOMYCIN JRNL TITL 2 ANALOGUES TARGETING 1-DEOXY-D-XYLULOSE-5-PHOSPHATE JRNL TITL 3 REDUCTOISOMERASE. JRNL REF J.MED.CHEM. V. 58 2988 2015 JRNL REFN ISSN 0022-2623 JRNL PMID 25781377 JRNL DOI 10.1021/JM5014264 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.65 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 3 NUMBER OF REFLECTIONS : 104856 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) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5530 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7345 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 388 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6552 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 714 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.03000 REMARK 3 B22 (A**2) : 0.07000 REMARK 3 B33 (A**2) : 1.68000 REMARK 3 B12 (A**2) : -0.71000 REMARK 3 B13 (A**2) : 0.23000 REMARK 3 B23 (A**2) : -1.59000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.092 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.091 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.076 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.284 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6831 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6629 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9237 ; 1.329 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15347 ; 0.766 ; 2.994 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 848 ; 5.525 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 302 ;37.499 ;26.424 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1289 ;16.587 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;14.580 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1053 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7680 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1494 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3335 ; 1.482 ; 2.020 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3334 ; 1.481 ; 2.019 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4184 ; 2.321 ; 3.020 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4185 ; 2.321 ; 3.022 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3496 ; 2.128 ; 2.351 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3497 ; 2.127 ; 2.351 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5048 ; 3.470 ; 3.408 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8595 ; 5.773 ;17.787 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8284 ; 5.586 ;17.354 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 77 A 486 1 REMARK 3 1 B 77 B 486 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 3948 ; 2.29 ; 0.50 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 4Y67 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206403. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : SI(311) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 110454 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 79.970 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.47800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 3AU8 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 8000, 20% V/V ETHYLENE REMARK 280 GLYCOL, 0.02M EACH OF SODIUM L-GLUTAMATE, DL-ALANINE, GLYCINE, REMARK 280 DL-LYSINE HCL, DL-SERINE, 0.1M MES/IMIDAZOLE PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING 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 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: 3790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 MET A 67 REMARK 465 ALA A 68 REMARK 465 HIS A 69 REMARK 465 HIS A 70 REMARK 465 HIS A 71 REMARK 465 HIS A 72 REMARK 465 HIS A 73 REMARK 465 HIS A 74 REMARK 465 LYS A 75 REMARK 465 LYS A 76 REMARK 465 SER A 487 REMARK 465 SER A 488 REMARK 465 MET B 67 REMARK 465 ALA B 68 REMARK 465 HIS B 69 REMARK 465 HIS B 70 REMARK 465 HIS B 71 REMARK 465 HIS B 72 REMARK 465 HIS B 73 REMARK 465 HIS B 74 REMARK 465 LYS B 75 REMARK 465 LYS B 76 REMARK 465 SER B 487 REMARK 465 SER B 488 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 NE2 GLN A 253 O HOH A 844 1.34 REMARK 500 O HOH B 601 O HOH B 640 1.56 REMARK 500 O HOH A 714 O HOH A 875 1.64 REMARK 500 OD1 ASN B 284 O HOH B 601 1.65 REMARK 500 O HOH B 705 O HOH B 859 1.80 REMARK 500 N PRO A 77 O HOH A 891 1.83 REMARK 500 O HOH A 833 O HOH A 933 1.85 REMARK 500 O HOH B 793 O HOH B 914 1.86 REMARK 500 O HOH B 781 O HOH B 824 1.96 REMARK 500 OD1 ASN A 92 O HOH A 951 1.98 REMARK 500 O HOH B 826 O HOH B 838 1.98 REMARK 500 O HOH A 875 O HOH A 927 2.02 REMARK 500 O HOH B 773 O HOH B 807 2.05 REMARK 500 O ILE A 179 O HOH A 956 2.06 REMARK 500 NZ LYS B 484 O HOH B 602 2.07 REMARK 500 O HOH A 755 O HOH A 946 2.07 REMARK 500 O HOH B 672 O HOH B 680 2.09 REMARK 500 OE1 GLU B 449 O HOH B 922 2.11 REMARK 500 NE2 GLN A 469 O HOH A 906 2.11 REMARK 500 O HOH A 922 O HOH A 936 2.14 REMARK 500 O HOH A 760 O HOH A 946 2.14 REMARK 500 O HOH B 838 O HOH B 867 2.15 REMARK 500 O HOH A 827 O HOH A 927 2.16 REMARK 500 OE1 GLU B 142 O HOH B 603 2.16 REMARK 500 O HOH B 720 O HOH B 921 2.17 REMARK 500 O HOH A 773 O HOH A 945 2.17 REMARK 500 OG SER A 457 O HOH A 876 2.18 REMARK 500 O HOH A 844 O HOH A 938 2.19 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 602 O HOH B 666 1666 2.11 REMARK 500 O HOH A 611 O HOH A 681 1655 2.18 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 115 -71.66 -70.60 REMARK 500 SER A 183 -132.13 55.33 REMARK 500 THR A 249 -152.77 -144.57 REMARK 500 SER A 342 169.43 166.47 REMARK 500 LYS A 349 2.75 85.02 REMARK 500 ASP A 359 115.00 -174.38 REMARK 500 SER A 387 -50.01 77.14 REMARK 500 ASN A 413 -141.97 49.03 REMARK 500 SER B 183 -139.28 54.49 REMARK 500 THR B 249 -154.90 -148.11 REMARK 500 ASN B 255 9.04 81.22 REMARK 500 SER B 342 168.44 169.53 REMARK 500 LYS B 349 3.41 82.72 REMARK 500 ASP B 359 112.41 -170.40 REMARK 500 SER B 387 -47.95 80.15 REMARK 500 ASN B 413 -138.20 47.61 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 MN A 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 231 OD1 REMARK 620 2 GLU A 233 OE1 97.5 REMARK 620 3 GLU A 315 OE2 100.6 96.6 REMARK 620 4 RC5 A 501 O12 127.4 134.4 84.2 REMARK 620 5 RC5 A 501 O10 84.0 103.2 159.0 77.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 502 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 231 OD1 REMARK 620 2 GLU B 233 OE1 97.4 REMARK 620 3 GLU B 315 OE2 99.1 97.4 REMARK 620 4 RC5 B 501 O12 124.3 137.3 85.6 REMARK 620 5 RC5 B 501 O10 82.2 101.3 160.9 78.2 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RC5 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue RC5 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 502 DBREF 4Y67 A 75 488 UNP Q8IKG4 DXR_PLAF7 75 488 DBREF 4Y67 B 75 488 UNP Q8IKG4 DXR_PLAF7 75 488 SEQADV 4Y67 MET A 67 UNP Q8IKG4 INITIATING METHIONINE SEQADV 4Y67 ALA A 68 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS A 69 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS A 70 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS A 71 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS A 72 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS A 73 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS A 74 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 MET B 67 UNP Q8IKG4 INITIATING METHIONINE SEQADV 4Y67 ALA B 68 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS B 69 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS B 70 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS B 71 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS B 72 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS B 73 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y67 HIS B 74 UNP Q8IKG4 EXPRESSION TAG SEQRES 1 A 422 MET ALA HIS HIS HIS HIS HIS HIS LYS LYS PRO ILE ASN SEQRES 2 A 422 VAL ALA ILE PHE GLY SER THR GLY SER ILE GLY THR ASN SEQRES 3 A 422 ALA LEU ASN ILE ILE ARG GLU CYS ASN LYS ILE GLU ASN SEQRES 4 A 422 VAL PHE ASN VAL LYS ALA LEU TYR VAL ASN LYS SER VAL SEQRES 5 A 422 ASN GLU LEU TYR GLU GLN ALA ARG GLU PHE LEU PRO GLU SEQRES 6 A 422 TYR LEU CYS ILE HIS ASP LYS SER VAL TYR GLU GLU LEU SEQRES 7 A 422 LYS GLU LEU VAL LYS ASN ILE LYS ASP TYR LYS PRO ILE SEQRES 8 A 422 ILE LEU CYS GLY ASP GLU GLY MET LYS GLU ILE CYS SER SEQRES 9 A 422 SER ASN SER ILE ASP LYS ILE VAL ILE GLY ILE ASP SER SEQRES 10 A 422 PHE GLN GLY LEU TYR SER THR MET TYR ALA ILE MET ASN SEQRES 11 A 422 ASN LYS ILE VAL ALA LEU ALA ASN LYS GLU SER ILE VAL SEQRES 12 A 422 SER ALA GLY PHE PHE LEU LYS LYS LEU LEU ASN ILE HIS SEQRES 13 A 422 LYS ASN ALA LYS ILE ILE PRO VAL ASP SER GLU HIS SER SEQRES 14 A 422 ALA ILE PHE GLN CYS LEU ASP ASN ASN LYS VAL LEU LYS SEQRES 15 A 422 THR LYS CYS LEU GLN ASP ASN PHE SER LYS ILE ASN ASN SEQRES 16 A 422 ILE ASN LYS ILE PHE LEU CYS SER SER GLY GLY PRO PHE SEQRES 17 A 422 GLN ASN LEU THR MET ASP GLU LEU LYS ASN VAL THR SER SEQRES 18 A 422 GLU ASN ALA LEU LYS HIS PRO LYS TRP LYS MET GLY LYS SEQRES 19 A 422 LYS ILE THR ILE ASP SER ALA THR MET MET ASN LYS GLY SEQRES 20 A 422 LEU GLU VAL ILE GLU THR HIS PHE LEU PHE ASP VAL ASP SEQRES 21 A 422 TYR ASN ASP ILE GLU VAL ILE VAL HIS LYS GLU CYS ILE SEQRES 22 A 422 ILE HIS SER CYS VAL GLU PHE ILE ASP LYS SER VAL ILE SEQRES 23 A 422 SER GLN MET TYR TYR PRO ASP MET GLN ILE PRO ILE LEU SEQRES 24 A 422 TYR SER LEU THR TRP PRO ASP ARG ILE LYS THR ASN LEU SEQRES 25 A 422 LYS PRO LEU ASP LEU ALA GLN VAL SER THR LEU THR PHE SEQRES 26 A 422 HIS LYS PRO SER LEU GLU HIS PHE PRO CYS ILE LYS LEU SEQRES 27 A 422 ALA TYR GLN ALA GLY ILE LYS GLY ASN PHE TYR PRO THR SEQRES 28 A 422 VAL LEU ASN ALA SER ASN GLU ILE ALA ASN ASN LEU PHE SEQRES 29 A 422 LEU ASN ASN LYS ILE LYS TYR PHE ASP ILE SER SER ILE SEQRES 30 A 422 ILE SER GLN VAL LEU GLU SER PHE ASN SER GLN LYS VAL SEQRES 31 A 422 SER GLU ASN SER GLU ASP LEU MET LYS GLN ILE LEU GLN SEQRES 32 A 422 ILE HIS SER TRP ALA LYS ASP LYS ALA THR ASP ILE TYR SEQRES 33 A 422 ASN LYS HIS ASN SER SER SEQRES 1 B 422 MET ALA HIS HIS HIS HIS HIS HIS LYS LYS PRO ILE ASN SEQRES 2 B 422 VAL ALA ILE PHE GLY SER THR GLY SER ILE GLY THR ASN SEQRES 3 B 422 ALA LEU ASN ILE ILE ARG GLU CYS ASN LYS ILE GLU ASN SEQRES 4 B 422 VAL PHE ASN VAL LYS ALA LEU TYR VAL ASN LYS SER VAL SEQRES 5 B 422 ASN GLU LEU TYR GLU GLN ALA ARG GLU PHE LEU PRO GLU SEQRES 6 B 422 TYR LEU CYS ILE HIS ASP LYS SER VAL TYR GLU GLU LEU SEQRES 7 B 422 LYS GLU LEU VAL LYS ASN ILE LYS ASP TYR LYS PRO ILE SEQRES 8 B 422 ILE LEU CYS GLY ASP GLU GLY MET LYS GLU ILE CYS SER SEQRES 9 B 422 SER ASN SER ILE ASP LYS ILE VAL ILE GLY ILE ASP SER SEQRES 10 B 422 PHE GLN GLY LEU TYR SER THR MET TYR ALA ILE MET ASN SEQRES 11 B 422 ASN LYS ILE VAL ALA LEU ALA ASN LYS GLU SER ILE VAL SEQRES 12 B 422 SER ALA GLY PHE PHE LEU LYS LYS LEU LEU ASN ILE HIS SEQRES 13 B 422 LYS ASN ALA LYS ILE ILE PRO VAL ASP SER GLU HIS SER SEQRES 14 B 422 ALA ILE PHE GLN CYS LEU ASP ASN ASN LYS VAL LEU LYS SEQRES 15 B 422 THR LYS CYS LEU GLN ASP ASN PHE SER LYS ILE ASN ASN SEQRES 16 B 422 ILE ASN LYS ILE PHE LEU CYS SER SER GLY GLY PRO PHE SEQRES 17 B 422 GLN ASN LEU THR MET ASP GLU LEU LYS ASN VAL THR SER SEQRES 18 B 422 GLU ASN ALA LEU LYS HIS PRO LYS TRP LYS MET GLY LYS SEQRES 19 B 422 LYS ILE THR ILE ASP SER ALA THR MET MET ASN LYS GLY SEQRES 20 B 422 LEU GLU VAL ILE GLU THR HIS PHE LEU PHE ASP VAL ASP SEQRES 21 B 422 TYR ASN ASP ILE GLU VAL ILE VAL HIS LYS GLU CYS ILE SEQRES 22 B 422 ILE HIS SER CYS VAL GLU PHE ILE ASP LYS SER VAL ILE SEQRES 23 B 422 SER GLN MET TYR TYR PRO ASP MET GLN ILE PRO ILE LEU SEQRES 24 B 422 TYR SER LEU THR TRP PRO ASP ARG ILE LYS THR ASN LEU SEQRES 25 B 422 LYS PRO LEU ASP LEU ALA GLN VAL SER THR LEU THR PHE SEQRES 26 B 422 HIS LYS PRO SER LEU GLU HIS PHE PRO CYS ILE LYS LEU SEQRES 27 B 422 ALA TYR GLN ALA GLY ILE LYS GLY ASN PHE TYR PRO THR SEQRES 28 B 422 VAL LEU ASN ALA SER ASN GLU ILE ALA ASN ASN LEU PHE SEQRES 29 B 422 LEU ASN ASN LYS ILE LYS TYR PHE ASP ILE SER SER ILE SEQRES 30 B 422 ILE SER GLN VAL LEU GLU SER PHE ASN SER GLN LYS VAL SEQRES 31 B 422 SER GLU ASN SER GLU ASP LEU MET LYS GLN ILE LEU GLN SEQRES 32 B 422 ILE HIS SER TRP ALA LYS ASP LYS ALA THR ASP ILE TYR SEQRES 33 B 422 ASN LYS HIS ASN SER SER HET RC5 A 501 21 HET MN A 502 1 HET RC5 B 501 21 HET MN B 502 1 HETNAM RC5 [(2R)-2-{2-[HYDROXY(METHYL)AMINO]-2-OXOETHYL}-5- HETNAM 2 RC5 PHENYLPENTYL]PHOSPHONIC ACID HETNAM MN MANGANESE (II) ION FORMUL 3 RC5 2(C14 H22 N O5 P) FORMUL 4 MN 2(MN 2+) FORMUL 7 HOH *714(H2 O) HELIX 1 AA1 GLY A 87 GLU A 104 1 18 HELIX 2 AA2 SER A 117 LEU A 129 1 13 HELIX 3 AA3 ASP A 137 SER A 139 5 3 HELIX 4 AA4 VAL A 140 LYS A 149 1 10 HELIX 5 AA5 GLY A 161 SER A 171 1 11 HELIX 6 AA6 ASP A 182 ASN A 196 1 15 HELIX 7 AA7 ASN A 204 HIS A 222 1 19 HELIX 8 AA8 ASP A 231 CYS A 240 1 10 HELIX 9 AA9 ASP A 242 LEU A 247 1 6 HELIX 10 AB1 ASN A 255 ASN A 260 1 6 HELIX 11 AB2 THR A 278 ASN A 284 1 7 HELIX 12 AB3 THR A 286 LYS A 292 1 7 HELIX 13 AB4 GLY A 299 MET A 309 1 11 HELIX 14 AB5 MET A 309 ASP A 324 1 16 HELIX 15 AB6 ASP A 326 ASN A 328 5 3 HELIX 16 AB7 MET A 360 TRP A 370 1 11 HELIX 17 AB8 ASP A 382 SER A 387 1 6 HELIX 18 AB9 PHE A 399 GLY A 412 1 14 HELIX 19 AC1 PHE A 414 ASN A 432 1 19 HELIX 20 AC2 LYS A 436 SER A 450 1 15 HELIX 21 AC3 ASN A 459 ASN A 486 1 28 HELIX 22 AC4 GLY B 87 GLU B 104 1 18 HELIX 23 AC5 SER B 117 LEU B 129 1 13 HELIX 24 AC6 ASP B 137 SER B 139 5 3 HELIX 25 AC7 VAL B 140 ASN B 150 1 11 HELIX 26 AC8 GLY B 161 SER B 171 1 11 HELIX 27 AC9 ASP B 182 ASN B 196 1 15 HELIX 28 AD1 ASN B 204 HIS B 222 1 19 HELIX 29 AD2 ASP B 231 CYS B 240 1 10 HELIX 30 AD3 ASP B 242 LEU B 247 1 6 HELIX 31 AD4 ASN B 255 ASN B 260 1 6 HELIX 32 AD5 THR B 278 VAL B 285 1 8 HELIX 33 AD6 THR B 286 LYS B 292 1 7 HELIX 34 AD7 GLY B 299 MET B 309 1 11 HELIX 35 AD8 MET B 309 ASP B 324 1 16 HELIX 36 AD9 ASP B 326 ASN B 328 5 3 HELIX 37 AE1 MET B 360 TRP B 370 1 11 HELIX 38 AE2 ASP B 382 SER B 387 1 6 HELIX 39 AE3 PHE B 399 GLY B 412 1 14 HELIX 40 AE4 PHE B 414 ASN B 432 1 19 HELIX 41 AE5 LYS B 436 PHE B 451 1 16 HELIX 42 AE6 ASN B 459 ASN B 486 1 28 SHEET 1 AA1 7 ILE A 157 CYS A 160 0 SHEET 2 AA1 7 TYR A 132 ILE A 135 1 N LEU A 133 O LEU A 159 SHEET 3 AA1 7 PHE A 107 VAL A 114 1 N LYS A 110 O TYR A 132 SHEET 4 AA1 7 ILE A 78 PHE A 83 1 N ILE A 78 O ASN A 108 SHEET 5 AA1 7 LYS A 176 ILE A 179 1 O VAL A 178 N ALA A 81 SHEET 6 AA1 7 ILE A 199 LEU A 202 1 O ALA A 201 N ILE A 179 SHEET 7 AA1 7 LYS A 226 PRO A 229 1 O LYS A 226 N VAL A 200 SHEET 1 AA2 8 ILE A 330 VAL A 334 0 SHEET 2 AA2 8 ILE A 262 SER A 269 1 N LEU A 267 O GLU A 331 SHEET 3 AA2 8 ILE A 340 PHE A 346 -1 O GLU A 345 N LYS A 264 SHEET 4 AA2 8 VAL A 351 MET A 355 -1 O ILE A 352 N VAL A 344 SHEET 5 AA2 8 VAL B 351 MET B 355 -1 O MET B 355 N VAL A 351 SHEET 6 AA2 8 ILE B 340 PHE B 346 -1 N VAL B 344 O ILE B 352 SHEET 7 AA2 8 ILE B 262 SER B 269 -1 N LYS B 264 O GLU B 345 SHEET 8 AA2 8 ILE B 330 VAL B 334 1 O GLU B 331 N LEU B 267 SHEET 1 AA3 2 THR A 388 THR A 390 0 SHEET 2 AA3 2 THR B 388 THR B 390 -1 O LEU B 389 N LEU A 389 SHEET 1 AA4 7 ILE B 157 CYS B 160 0 SHEET 2 AA4 7 TYR B 132 ILE B 135 1 N LEU B 133 O LEU B 159 SHEET 3 AA4 7 PHE B 107 VAL B 114 1 N LYS B 110 O TYR B 132 SHEET 4 AA4 7 ILE B 78 PHE B 83 1 N ILE B 78 O ASN B 108 SHEET 5 AA4 7 LYS B 176 ILE B 179 1 O VAL B 178 N ALA B 81 SHEET 6 AA4 7 ILE B 199 LEU B 202 1 O ALA B 201 N ILE B 179 SHEET 7 AA4 7 LYS B 226 PRO B 229 1 O LYS B 226 N VAL B 200 LINK OD1 ASP A 231 MN MN A 502 1555 1555 2.13 LINK OE1 GLU A 233 MN MN A 502 1555 1555 2.10 LINK OE2 GLU A 315 MN MN A 502 1555 1555 2.07 LINK O12 RC5 A 501 MN MN A 502 1555 1555 2.16 LINK O10 RC5 A 501 MN MN A 502 1555 1555 2.14 LINK OD1 ASP B 231 MN MN B 502 1555 1555 2.11 LINK OE1 GLU B 233 MN MN B 502 1555 1555 2.10 LINK OE2 GLU B 315 MN MN B 502 1555 1555 2.08 LINK O12 RC5 B 501 MN MN B 502 1555 1555 2.14 LINK O10 RC5 B 501 MN MN B 502 1555 1555 2.15 CISPEP 1 TRP A 370 PRO A 371 0 5.93 CISPEP 2 TRP B 370 PRO B 371 0 5.91 SITE 1 AC1 17 LYS A 205 ASP A 231 SER A 232 GLU A 233 SITE 2 AC1 17 SER A 269 SER A 270 TRP A 296 SER A 306 SITE 3 AC1 17 ASN A 311 LYS A 312 GLU A 315 HIS A 341 SITE 4 AC1 17 ASP A 359 MN A 502 HOH A 705 HOH A 728 SITE 5 AC1 17 HOH A 805 SITE 1 AC2 5 LYS A 205 ASP A 231 GLU A 233 GLU A 315 SITE 2 AC2 5 RC5 A 501 SITE 1 AC3 17 LYS B 205 ASP B 231 SER B 232 GLU B 233 SITE 2 AC3 17 SER B 269 SER B 270 TRP B 296 SER B 306 SITE 3 AC3 17 ASN B 311 LYS B 312 GLU B 315 HIS B 341 SITE 4 AC3 17 ASP B 359 MN B 502 HOH B 697 HOH B 716 SITE 5 AC3 17 HOH B 719 SITE 1 AC4 5 LYS B 205 ASP B 231 GLU B 233 GLU B 315 SITE 2 AC4 5 RC5 B 501 CRYST1 51.570 56.465 86.024 104.11 103.25 100.16 P 1 2 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 0.019391 0.003474 0.005860 0.00000 SCALE2 0.000000 0.017992 0.005588 0.00000 SCALE3 0.000000 0.000000 0.012505 0.00000