HEADER ISOMERASE 14-FEB-03 1NYW TITLE THE HIGH RESOLUTION STRUCTURES OF RMLC FROM STREPTOCCUS SUIS IN TITLE 2 COMPLEX WITH DTDP-D-GLUCOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DTDP-4-DEHYDRORHAMNOSE 3,5-EPIMERASE; COMPND 5 EC: 5.1.3.13; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS SUIS; SOURCE 3 ORGANISM_TAXID: 1307; SOURCE 4 STRAIN: SEROTYPE 2; SOURCE 5 GENE: RMLC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21(+) KEYWDS JELLY ROLL-LIKE STRUCTURE; BETA SHEET, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.DONG,L.L.MAJOR,A.ALLEN,W.BLANKENFELDT,D.MASKELL,J.H.NAISMITH REVDAT 4 14-FEB-24 1NYW 1 REMARK REVDAT 3 23-MAY-12 1NYW 1 HETATM REMARK VERSN REVDAT 2 24-FEB-09 1NYW 1 VERSN REVDAT 1 24-JUN-03 1NYW 0 JRNL AUTH C.DONG,L.L.MAJOR,A.ALLEN,W.BLANKENFELDT,D.MASKELL, JRNL AUTH 2 J.H.NAISMITH JRNL TITL HIGH-RESOLUTION STRUCTURES OF RMLC FROM STREPTOCOCCUS SUIS JRNL TITL 2 IN COMPLEX WITH SUBSTRATE ANALOGS LOCATE THE ACTIVE SITE OF JRNL TITL 3 THIS CLASS OF ENZYME JRNL REF STRUCTURE V. 11 715 2003 JRNL REFN ISSN 0969-2126 JRNL PMID 12791259 JRNL DOI 10.1016/S0969-2126(03)00098-4 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 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) : 29.88 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 41144 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2190 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) : 2372 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.80 REMARK 3 BIN R VALUE (WORKING SET) : 0.3120 REMARK 3 BIN FREE R VALUE SET COUNT : 114 REMARK 3 BIN FREE R VALUE : 0.3020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3145 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 507 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.52000 REMARK 3 B22 (A**2) : -0.88000 REMARK 3 B33 (A**2) : 0.33000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.200 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.346 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3318 ; 0.019 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2868 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4513 ; 1.822 ; 1.971 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6712 ; 0.979 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 389 ; 6.625 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 468 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3665 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 695 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 667 ; 0.202 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3412 ; 0.259 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1866 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 373 ; 0.206 ; 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): 31 ; 0.170 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 89 ; 0.244 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 70 ; 0.229 ; 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): 1943 ; 1.593 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3125 ; 2.043 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1375 ; 2.688 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1388 ; 3.680 ; 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): 3318 ; 1.627 ; 2.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 507 ; 3.516 ; 2.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3223 ; 2.309 ; 2.000 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 : 19 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 22 A 27 2 REMARK 3 1 B 22 B 27 2 REMARK 3 2 A 60 A 67 2 REMARK 3 2 B 60 B 67 2 REMARK 3 3 A 71 A 77 4 REMARK 3 3 B 71 B 77 4 REMARK 3 4 A 80 A 86 2 REMARK 3 4 B 80 B 86 2 REMARK 3 5 A 90 A 101 2 REMARK 3 5 B 90 B 101 2 REMARK 3 6 A 106 A 113 2 REMARK 3 6 B 106 B 113 2 REMARK 3 7 A 116 A 122 2 REMARK 3 7 B 116 B 122 2 REMARK 3 8 A 125 A 131 2 REMARK 3 8 B 125 B 131 2 REMARK 3 9 A 136 A 142 2 REMARK 3 9 B 136 B 142 2 REMARK 3 10 A 6 A 21 4 REMARK 3 10 B 6 B 21 4 REMARK 3 11 A 27 A 59 4 REMARK 3 11 B 27 B 59 4 REMARK 3 12 A 68 A 70 6 REMARK 3 12 B 68 B 70 6 REMARK 3 13 A 78 A 79 6 REMARK 3 13 B 78 B 79 6 REMARK 3 14 A 87 A 89 6 REMARK 3 14 B 87 B 89 6 REMARK 3 15 A 102 A 105 6 REMARK 3 15 B 102 B 105 6 REMARK 3 16 A 114 A 115 6 REMARK 3 16 B 114 B 115 6 REMARK 3 17 A 123 A 124 6 REMARK 3 17 B 123 B 124 6 REMARK 3 18 A 132 A 135 6 REMARK 3 18 B 132 B 135 6 REMARK 3 19 A 143 A 197 5 REMARK 3 19 B 143 B 197 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 944 ; 0.07 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 1725 ; 0.78 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 282 ; 0.73 ; 5.00 REMARK 3 TIGHT THERMAL 1 A (A**2): 944 ; 0.74 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1725 ; 1.17 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 282 ; 1.63 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 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 4 A 197 REMARK 3 ORIGIN FOR THE GROUP (A): -2.1590 -10.7100 20.4170 REMARK 3 T TENSOR REMARK 3 T11: 0.0740 T22: 0.0034 REMARK 3 T33: 0.0567 T12: -0.0064 REMARK 3 T13: -0.0251 T23: -0.0095 REMARK 3 L TENSOR REMARK 3 L11: 0.6712 L22: 1.0218 REMARK 3 L33: 1.0467 L12: 0.3541 REMARK 3 L13: -0.2546 L23: 0.0906 REMARK 3 S TENSOR REMARK 3 S11: 0.0443 S12: 0.0408 S13: -0.1093 REMARK 3 S21: 0.0199 S22: 0.0327 S23: 0.0042 REMARK 3 S31: 0.0893 S32: -0.0506 S33: -0.0771 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 : B 3 B 197 REMARK 3 ORIGIN FOR THE GROUP (A): 14.4630 10.2460 14.0590 REMARK 3 T TENSOR REMARK 3 T11: 0.1296 T22: 0.0580 REMARK 3 T33: 0.0157 T12: -0.0419 REMARK 3 T13: 0.0181 T23: -0.0131 REMARK 3 L TENSOR REMARK 3 L11: 1.3468 L22: 0.7063 REMARK 3 L33: 0.4620 L12: 0.3084 REMARK 3 L13: 0.0005 L23: 0.0231 REMARK 3 S TENSOR REMARK 3 S11: -0.0355 S12: 0.1362 S13: 0.0164 REMARK 3 S21: -0.0699 S22: 0.0637 S23: -0.0728 REMARK 3 S31: -0.1186 S32: 0.1328 S33: -0.0282 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 1NYW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018365. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 8.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : DIAMOND(111), GE(220), TOROIDAL REMARK 200 MIRROR REMARK 200 OPTICS : DIAMOND REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA, CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43352 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 29.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 5.2000 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 (%) : 79.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : 0.29200 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 25.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 4 MM NICL2,40% PEG 2000, REMARK 280 PH 8.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 23.94750 REMARK 290 SMTRY3 2 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: 5600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 1 REMARK 465 THR A 2 REMARK 465 GLU A 3 REMARK 465 MET B 1 REMARK 465 THR 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 9017 O HOH A 9139 1.46 REMARK 500 OG SER B 85 O HOH B 5005 1.59 REMARK 500 NZ LYS B 82 O HOH B 5066 1.60 REMARK 500 O HOH A 9136 O HOH A 9157 2.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 165 CB - CG - OD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ASP A 188 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 196 CB - CG - OD2 ANGL. DEV. = 6.1 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 LYS A 69 129.16 -35.50 REMARK 500 ASP A 88 -155.15 -123.52 REMARK 500 ASN A 170 81.53 -156.55 REMARK 500 PHE B 5 -47.89 -130.26 REMARK 500 ASN B 70 -7.19 80.47 REMARK 500 PRO B 79 45.81 -82.43 REMARK 500 ASP B 88 -159.03 -118.62 REMARK 500 ASP B 114 -165.18 -124.41 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 DAU B 5001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DAU A 9001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NXM RELATED DB: PDB REMARK 900 APO STRUCTURE OF RMLC FROM STREPTOCCUS SUIS REMARK 900 RELATED ID: 1NZC RELATED DB: PDB REMARK 900 RMLC STRUCTURE FROM STREPTOCOCCUS SUIS 2 IN COMPLEX WITH THYMIDINE- REMARK 900 5'-DIPHOSPHO-BETA-D-XYLOSE DBREF 1NYW A 1 197 UNP Q8GIQ0 Q8GIQ0_STRSU 1 197 DBREF 1NYW B 1 197 UNP Q8GIQ0 Q8GIQ0_STRSU 1 197 SEQRES 1 A 197 MET THR GLU ASN PHE PHE GLY LYS THR LEU ALA ALA ARG SEQRES 2 A 197 PRO VAL GLU ALA ILE PRO GLY MET LEU GLU PHE ASP ILE SEQRES 3 A 197 PRO VAL HIS GLY ASP ASN ARG GLY TRP PHE LYS GLU ASN SEQRES 4 A 197 PHE GLN LYS GLU LYS MET LEU PRO LEU GLY PHE PRO GLU SEQRES 5 A 197 SER PHE PHE ALA GLU GLY LYS LEU GLN ASN ASN VAL SER SEQRES 6 A 197 PHE SER ARG LYS ASN VAL LEU ARG GLY LEU HIS ALA GLU SEQRES 7 A 197 PRO TRP ASP LYS TYR ILE SER VAL ALA ASP GLY GLY LYS SEQRES 8 A 197 VAL LEU GLY THR TRP VAL ASP LEU ARG GLU GLY GLU THR SEQRES 9 A 197 PHE GLY ASN THR TYR GLN THR VAL ILE ASP ALA SER LYS SEQRES 10 A 197 SER ILE PHE VAL PRO ARG GLY VAL ALA ASN GLY PHE GLN SEQRES 11 A 197 VAL LEU SER ASP PHE VAL ALA TYR SER TYR LEU VAL ASN SEQRES 12 A 197 ASP TYR TRP ALA LEU GLU LEU LYS PRO LYS TYR ALA PHE SEQRES 13 A 197 VAL ASN TYR ALA ASP PRO SER LEU ASP ILE LYS TRP GLU SEQRES 14 A 197 ASN LEU GLU GLU ALA GLU VAL SER GLU ALA ASP GLU ASN SEQRES 15 A 197 HIS PRO PHE LEU LYS ASP VAL LYS PRO LEU ARG LYS GLU SEQRES 16 A 197 ASP LEU SEQRES 1 B 197 MET THR GLU ASN PHE PHE GLY LYS THR LEU ALA ALA ARG SEQRES 2 B 197 PRO VAL GLU ALA ILE PRO GLY MET LEU GLU PHE ASP ILE SEQRES 3 B 197 PRO VAL HIS GLY ASP ASN ARG GLY TRP PHE LYS GLU ASN SEQRES 4 B 197 PHE GLN LYS GLU LYS MET LEU PRO LEU GLY PHE PRO GLU SEQRES 5 B 197 SER PHE PHE ALA GLU GLY LYS LEU GLN ASN ASN VAL SER SEQRES 6 B 197 PHE SER ARG LYS ASN VAL LEU ARG GLY LEU HIS ALA GLU SEQRES 7 B 197 PRO TRP ASP LYS TYR ILE SER VAL ALA ASP GLY GLY LYS SEQRES 8 B 197 VAL LEU GLY THR TRP VAL ASP LEU ARG GLU GLY GLU THR SEQRES 9 B 197 PHE GLY ASN THR TYR GLN THR VAL ILE ASP ALA SER LYS SEQRES 10 B 197 SER ILE PHE VAL PRO ARG GLY VAL ALA ASN GLY PHE GLN SEQRES 11 B 197 VAL LEU SER ASP PHE VAL ALA TYR SER TYR LEU VAL ASN SEQRES 12 B 197 ASP TYR TRP ALA LEU GLU LEU LYS PRO LYS TYR ALA PHE SEQRES 13 B 197 VAL ASN TYR ALA ASP PRO SER LEU ASP ILE LYS TRP GLU SEQRES 14 B 197 ASN LEU GLU GLU ALA GLU VAL SER GLU ALA ASP GLU ASN SEQRES 15 B 197 HIS PRO PHE LEU LYS ASP VAL LYS PRO LEU ARG LYS GLU SEQRES 16 B 197 ASP LEU HET DAU A9001 36 HET DAU B5001 36 HETNAM DAU 2'DEOXY-THYMIDINE-5'-DIPHOSPHO-ALPHA-D-GLUCOSE FORMUL 3 DAU 2(C16 H26 N2 O16 P2) FORMUL 5 HOH *507(H2 O) HELIX 1 1 LYS A 42 LEU A 46 1 5 HELIX 2 2 PRO A 47 GLY A 49 5 3 HELIX 3 3 PRO A 51 PHE A 55 5 5 HELIX 4 4 ALA A 147 TYR A 154 5 8 HELIX 5 5 SER A 177 ASN A 182 1 6 HELIX 6 6 PHE A 185 VAL A 189 5 5 HELIX 7 7 LYS B 42 LEU B 46 1 5 HELIX 8 8 PRO B 47 GLY B 49 5 3 HELIX 9 9 PRO B 51 ALA B 56 5 6 HELIX 10 10 ALA B 147 TYR B 154 5 8 HELIX 11 11 SER B 177 ASN B 182 1 6 HELIX 12 12 PHE B 185 VAL B 189 5 5 SHEET 1 A 8 ALA A 11 PRO A 14 0 SHEET 2 A 8 LEU A 22 ASP A 25 -1 O ASP A 25 N ALA A 11 SHEET 3 A 8 LYS A 117 VAL A 121 -1 O PHE A 120 N LEU A 22 SHEET 4 A 8 LYS A 82 VAL A 86 -1 N LYS A 82 O VAL A 121 SHEET 5 A 8 PHE A 135 VAL A 142 -1 O LEU A 141 N TYR A 83 SHEET 6 A 8 GLN A 61 ARG A 68 -1 N SER A 65 O TYR A 138 SHEET 7 A 8 GLY B 34 GLN B 41 -1 O LYS B 37 N VAL A 64 SHEET 8 A 8 VAL B 28 ASP B 31 -1 N HIS B 29 O PHE B 36 SHEET 1 B 8 VAL A 28 ASP A 31 0 SHEET 2 B 8 GLY A 34 GLN A 41 -1 O PHE A 36 N HIS A 29 SHEET 3 B 8 GLN B 61 ARG B 68 -1 O ASN B 62 N PHE A 40 SHEET 4 B 8 PHE B 135 VAL B 142 -1 O TYR B 138 N SER B 65 SHEET 5 B 8 LYS B 82 VAL B 86 -1 N TYR B 83 O LEU B 141 SHEET 6 B 8 LYS B 117 VAL B 121 -1 O VAL B 121 N LYS B 82 SHEET 7 B 8 LEU B 22 ASP B 25 -1 N LEU B 22 O PHE B 120 SHEET 8 B 8 ALA B 11 PRO B 14 -1 N ARG B 13 O GLU B 23 SHEET 1 C 5 THR A 108 ILE A 113 0 SHEET 2 C 5 VAL A 92 ASP A 98 -1 N VAL A 92 O ILE A 113 SHEET 3 C 5 VAL A 125 VAL A 131 -1 O ALA A 126 N VAL A 97 SHEET 4 C 5 LEU A 72 ALA A 77 -1 N ARG A 73 O PHE A 129 SHEET 5 C 5 ALA A 155 PHE A 156 -1 O ALA A 155 N ALA A 77 SHEET 1 D 5 THR B 108 ILE B 113 0 SHEET 2 D 5 VAL B 92 ASP B 98 -1 N GLY B 94 O THR B 111 SHEET 3 D 5 VAL B 125 VAL B 131 -1 O ALA B 126 N VAL B 97 SHEET 4 D 5 LEU B 72 ALA B 77 -1 N ARG B 73 O PHE B 129 SHEET 5 D 5 ALA B 155 PHE B 156 -1 O ALA B 155 N ALA B 77 CISPEP 1 GLY A 74 LEU A 75 0 -2.73 CISPEP 2 GLY B 74 LEU B 75 0 3.21 SITE 1 AC1 20 ARG A 33 PHE A 36 GLU A 38 GLN B 61 SITE 2 AC1 20 ASN B 63 SER B 65 ARG B 73 HIS B 76 SITE 3 AC1 20 GLU B 78 LYS B 82 ASN B 127 TYR B 140 SITE 4 AC1 20 TRP B 146 LYS B 151 HOH B5024 HOH B5095 SITE 5 AC1 20 HOH B5110 HOH B5152 HOH B5180 HOH B5237 SITE 1 AC2 24 GLN A 61 ASN A 63 SER A 65 ARG A 73 SITE 2 AC2 24 HIS A 76 GLU A 78 LYS A 82 ASN A 127 SITE 3 AC2 24 TYR A 140 TRP A 146 HOH A9005 HOH A9024 SITE 4 AC2 24 HOH A9027 HOH A9032 HOH A9036 HOH A9037 SITE 5 AC2 24 HOH A9047 HOH A9156 HIS B 29 ARG B 33 SITE 6 AC2 24 PHE B 36 GLU B 38 HOH B5060 HOH B5097 CRYST1 50.586 47.895 72.417 90.00 99.02 90.00 P 1 21 1 4 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 0.019768 0.000000 0.003138 0.00000 SCALE2 0.000000 0.020879 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013982 0.00000