HEADER OXIDOREDUCTASE 13-FEB-15 4Y6S TITLE STRUCTURE OF PLASMODIUM FALCIPARUM DXR IN COMPLEX WITH A BETA- TITLE 2 SUBSTITUTED FOSMIDOMYCIN ANALOGUE, RC134, 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 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM (ISOLATE 3D7); SOURCE 3 ORGANISM_TAXID: 36329; SOURCE 4 STRAIN: ISOLATE 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 2 22-APR-15 4Y6S 1 JRNL REVDAT 1 01-APR-15 4Y6S 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. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 44433 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2377 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.15 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3095 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 160 REMARK 3 BIN FREE R VALUE : 0.3120 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 : 40 REMARK 3 SOLVENT ATOMS : 251 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.58000 REMARK 3 B22 (A**2) : 5.11000 REMARK 3 B33 (A**2) : -3.12000 REMARK 3 B12 (A**2) : 1.82000 REMARK 3 B13 (A**2) : -1.30000 REMARK 3 B23 (A**2) : -0.53000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.300 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.216 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.176 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.824 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6726 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6556 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9072 ; 1.372 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15152 ; 1.343 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 818 ; 5.803 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 296 ;39.225 ;26.351 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1274 ;17.370 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;16.367 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1036 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7486 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1464 ; 0.004 ; 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): 3278 ; 1.325 ; 3.227 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3277 ; 1.323 ; 3.226 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4094 ; 2.251 ; 4.833 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4095 ; 2.251 ; 4.834 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3448 ; 1.374 ; 3.452 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3449 ; 1.374 ; 3.452 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4979 ; 2.457 ; 5.083 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8115 ; 4.229 ;25.901 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8057 ; 4.185 ;25.852 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 B (A**2): 3898 ; 5.09 ; 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 4Y6S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000206947. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-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 : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46811 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.33500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 20,000 20% V/V PEG MME REMARK 280 550, 0.02M EACH OF SODIUM L-GLUTAMATE, DL-ALANINE, GLYCINE, DL- REMARK 280 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 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 O ASN A 486 O HOH A 601 1.79 REMARK 500 O HOH A 658 O HOH B 641 2.14 REMARK 500 O ASP A 359 O HOH A 727 2.17 REMARK 500 OE2 GLU A 424 O HOH A 686 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 -73.79 -69.86 REMARK 500 LYS A 116 37.28 -147.38 REMARK 500 SER A 183 -169.28 67.46 REMARK 500 THR A 249 -155.58 -148.95 REMARK 500 ASN A 255 -1.70 84.03 REMARK 500 SER A 342 170.93 171.74 REMARK 500 LYS A 349 -2.88 92.82 REMARK 500 SER A 387 -54.08 80.50 REMARK 500 ASN A 413 -137.32 52.80 REMARK 500 HIS A 485 -93.88 -46.14 REMARK 500 LYS B 116 13.91 -148.31 REMARK 500 ASP B 137 108.76 -53.70 REMARK 500 ASN B 150 24.66 -77.05 REMARK 500 ASP B 153 55.40 27.86 REMARK 500 TYR B 154 123.15 -172.05 REMARK 500 THR B 249 -156.59 -149.41 REMARK 500 ASN B 255 -1.78 81.89 REMARK 500 SER B 342 166.41 162.69 REMARK 500 LYS B 349 -2.73 89.72 REMARK 500 TRP B 370 141.41 -39.99 REMARK 500 SER B 387 -48.21 76.75 REMARK 500 ASN B 413 -132.11 59.21 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 ILE B 181 ASP B 182 -143.31 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 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 231 OD1 REMARK 620 2 GLU A 233 OE1 93.1 REMARK 620 3 GLU A 233 OE2 144.6 53.0 REMARK 620 4 GLU A 315 OE2 106.8 93.9 87.8 REMARK 620 5 48S A 502 O10 82.6 99.0 91.9 163.7 REMARK 620 6 48S A 502 O12 125.6 139.2 86.3 87.1 76.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 231 OD1 REMARK 620 2 GLU B 233 OE1 92.2 REMARK 620 3 GLU B 233 OE2 144.3 53.5 REMARK 620 4 GLU B 315 OE2 97.9 87.4 90.7 REMARK 620 5 48S B 502 O12 120.1 147.4 94.0 91.4 REMARK 620 6 48S B 502 O10 87.3 101.2 90.2 169.9 78.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 48S A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 48S B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Y67 RELATED DB: PDB REMARK 900 4Y67 CONTAINS THE SAME PROTEIN COMPLEXED WITH RC176 REMARK 900 RELATED ID: 4Y6P RELATED DB: PDB REMARK 900 4Y6P CONTAINS THE SAME PROTEIN COMPLEXED WITH RC177 REMARK 900 RELATED ID: 4Y6R RELATED DB: PDB REMARK 900 4Y6R CONTAINS THE SAME PROTEIN COMPLEXED WITH RC137 DBREF 4Y6S A 75 488 UNP Q8IKG4 DXR_PLAF7 75 488 DBREF 4Y6S B 75 488 UNP Q8IKG4 DXR_PLAF7 75 488 SEQADV 4Y6S MET A 67 UNP Q8IKG4 INITIATING METHIONINE SEQADV 4Y6S ALA A 68 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS A 69 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS A 70 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS A 71 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS A 72 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS A 73 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS A 74 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S MET B 67 UNP Q8IKG4 INITIATING METHIONINE SEQADV 4Y6S ALA B 68 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS B 69 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS B 70 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS B 71 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS B 72 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S HIS B 73 UNP Q8IKG4 EXPRESSION TAG SEQADV 4Y6S 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 MN A 501 1 HET 48S A 502 19 HET MN B 501 1 HET 48S B 502 19 HETNAM MN MANGANESE (II) ION HETNAM 48S [(2R)-4-[HYDROXY(METHYL)AMINO]-2-(4-METHYLPHENYL)-4- HETNAM 2 48S OXOBUTYL]PHOSPHONIC ACID FORMUL 3 MN 2(MN 2+) FORMUL 4 48S 2(C12 H18 N O5 P) FORMUL 7 HOH *251(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 LEU A 291 1 6 HELIX 13 AB4 GLY A 299 THR A 308 1 10 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 PHE A 451 1 16 HELIX 21 AC3 ASN A 459 HIS A 485 1 27 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 SER B 183 GLN B 185 5 3 HELIX 28 AD1 GLY B 186 ASN B 196 1 11 HELIX 29 AD2 ASN B 204 HIS B 222 1 19 HELIX 30 AD3 ASP B 231 CYS B 240 1 10 HELIX 31 AD4 ASP B 242 LEU B 247 1 6 HELIX 32 AD5 ASN B 255 ASN B 260 1 6 HELIX 33 AD6 THR B 278 LYS B 283 1 6 HELIX 34 AD7 THR B 286 LEU B 291 1 6 HELIX 35 AD8 GLY B 299 THR B 308 1 10 HELIX 36 AD9 MET B 309 ASP B 324 1 16 HELIX 37 AE1 ASP B 326 ASN B 328 5 3 HELIX 38 AE2 MET B 360 TRP B 370 1 11 HELIX 39 AE3 ASP B 382 SER B 387 1 6 HELIX 40 AE4 PHE B 399 GLY B 412 1 14 HELIX 41 AE5 PHE B 414 ASN B 432 1 19 HELIX 42 AE6 LYS B 436 SER B 450 1 15 HELIX 43 AE7 ASN B 459 HIS B 485 1 27 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 PHE A 83 SHEET 6 AA1 7 ILE A 199 LEU A 202 1 O ILE A 199 N ILE A 177 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 ILE A 265 O GLU A 331 SHEET 3 AA2 8 ILE A 340 PHE A 346 -1 O GLU A 345 N ASN A 263 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 VAL B 351 N MET A 355 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 ASN B 263 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 ILE B 157 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 82 O ALA B 111 SHEET 5 AA4 7 LYS B 176 ILE B 179 1 O VAL B 178 N PHE B 83 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 501 1555 1555 2.14 LINK OE1 GLU A 233 MN MN A 501 1555 1555 2.15 LINK OE2 GLU A 233 MN MN A 501 1555 1555 2.64 LINK OE2 GLU A 315 MN MN A 501 1555 1555 2.15 LINK OD1 ASP B 231 MN MN B 501 1555 1555 2.14 LINK OE1 GLU B 233 MN MN B 501 1555 1555 2.15 LINK OE2 GLU B 233 MN MN B 501 1555 1555 2.62 LINK OE2 GLU B 315 MN MN B 501 1555 1555 2.13 LINK MN MN A 501 O10 48S A 502 1555 1555 2.15 LINK MN MN A 501 O12 48S A 502 1555 1555 2.18 LINK MN MN B 501 O12 48S B 502 1555 1555 2.18 LINK MN MN B 501 O10 48S B 502 1555 1555 2.14 CISPEP 1 TRP A 370 PRO A 371 0 3.74 CISPEP 2 TRP B 370 PRO B 371 0 0.86 SITE 1 AC1 5 LYS A 205 ASP A 231 GLU A 233 GLU A 315 SITE 2 AC1 5 48S A 502 SITE 1 AC2 15 ASP A 231 SER A 232 GLU A 233 SER A 269 SITE 2 AC2 15 SER A 270 TRP A 296 MET A 298 SER A 306 SITE 3 AC2 15 ASN A 311 LYS A 312 GLU A 315 MN A 501 SITE 4 AC2 15 HOH A 647 HOH A 725 HOH A 742 SITE 1 AC3 5 LYS B 205 ASP B 231 GLU B 233 GLU B 315 SITE 2 AC3 5 48S B 502 SITE 1 AC4 16 LYS B 205 ASP B 231 SER B 232 GLU B 233 SITE 2 AC4 16 SER B 269 SER B 270 TRP B 296 MET B 298 SITE 3 AC4 16 ILE B 302 SER B 306 ASN B 311 LYS B 312 SITE 4 AC4 16 GLU B 315 MN B 501 HOH B 674 HOH B 706 CRYST1 51.396 54.963 85.054 89.41 105.52 107.28 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 0.019457 0.006054 0.005874 0.00000 SCALE2 0.000000 0.019054 0.001436 0.00000 SCALE3 0.000000 0.000000 0.012237 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 0.718074 0.320269 -0.617898 -3.61856 1 MTRIX2 2 0.331734 -0.937987 -0.100661 36.29359 1 MTRIX3 2 -0.611819 -0.132696 -0.779788 9.54288 1