PDB Short entry for 1NXM HEADER ISOMERASE 11-FEB-03 1NXM TITLE THE HIGH RESOLUTION STRUCTURES OF RMLC FROM STREPTOCOCCUS SUIS 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 3 14-FEB-24 1NXM 1 REMARK REVDAT 2 24-FEB-09 1NXM 1 VERSN REVDAT 1 24-JUN-03 1NXM 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. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.39 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.678 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 79880 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4225 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5229 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1950 REMARK 3 BIN FREE R VALUE SET COUNT : 257 REMARK 3 BIN FREE R VALUE : 0.2200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3136 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 633 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.11 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : 0.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.23000 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): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3333 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2902 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4532 ; 1.481 ; 1.941 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6790 ; 0.836 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 407 ; 6.702 ; 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): 461 ; 0.091 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3793 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 723 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 628 ; 0.218 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3433 ; 0.259 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1892 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 444 ; 0.176 ; 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): 17 ; 0.232 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 69 ; 0.335 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 50 ; 0.222 ; 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): 1997 ; 1.265 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3224 ; 1.875 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1336 ; 2.706 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1308 ; 3.977 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 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 ; 0.06 ; 0.05 REMARK 3 MEDIUM POSITIONAL 1 A (A): 1589 ; 0.53 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 282 ; 0.56 ; 5.00 REMARK 3 TIGHT THERMAL 1 A (A**2): 944 ; 0.38 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1589 ; 1.16 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 282 ; 2.75 ; 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): 9.8450 9.3450 2.7130 REMARK 3 T TENSOR REMARK 3 T11: 0.0320 T22: 0.0282 REMARK 3 T33: 0.0076 T12: 0.0019 REMARK 3 T13: 0.0081 T23: -0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.6681 L22: 0.8807 REMARK 3 L33: 0.5827 L12: 0.1422 REMARK 3 L13: -0.0653 L23: -0.1581 REMARK 3 S TENSOR REMARK 3 S11: -0.0295 S12: 0.0422 S13: 0.0192 REMARK 3 S21: -0.0444 S22: 0.0190 S23: -0.0584 REMARK 3 S31: -0.0166 S32: -0.0271 S33: 0.0105 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 4 B 197 REMARK 3 ORIGIN FOR THE GROUP (A): 2.9650 -9.5640 22.8290 REMARK 3 T TENSOR REMARK 3 T11: 0.0879 T22: 0.1130 REMARK 3 T33: 0.1119 T12: -0.0281 REMARK 3 T13: -0.0268 T23: 0.0536 REMARK 3 L TENSOR REMARK 3 L11: 1.6056 L22: 0.9011 REMARK 3 L33: 0.6713 L12: 0.4699 REMARK 3 L13: 0.3298 L23: 0.1831 REMARK 3 S TENSOR REMARK 3 S11: 0.1590 S12: -0.2078 S13: -0.3362 REMARK 3 S21: 0.1271 S22: -0.0877 S23: -0.0699 REMARK 3 S31: 0.1059 S32: -0.1229 S33: -0.0712 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 : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NXM 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_1000018322. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-NOV-01 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 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) REMARK 200 OPTICS : NULL 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 : 84137 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 28.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.100 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : 0.03900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.21300 REMARK 200 R SYM FOR SHELL (I) : 0.24100 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG 2000, 0.2 M MGCL2, 0.1 M TRIS REMARK 280 , 4 MM NICL2, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K 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 40.81200 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: 2700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 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 465 GLU B 3 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 547 O HOH A 553 1.85 REMARK 500 O HOH A 282 O HOH A 407 2.01 REMARK 500 ND1 HIS A 76 O HOH A 553 2.05 REMARK 500 O HOH A 361 O HOH A 554 2.11 REMARK 500 O HOH A 306 O HOH A 550 2.16 REMARK 500 O HOH A 263 O HOH A 547 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 351 O HOH A 556 2545 1.73 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 SER B 85 CB SER B 85 OG 0.081 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 PHE A 5 -52.66 -135.53 REMARK 500 ASN A 70 -8.58 78.89 REMARK 500 ASP A 88 -160.09 -118.59 REMARK 500 ASN B 70 -6.59 81.71 REMARK 500 PRO B 79 5.70 -69.08 REMARK 500 ASP B 88 -159.90 -119.72 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NYW RELATED DB: PDB REMARK 900 RMLC STRUCTURE FROM STREPTOCOCCUS SUIS 2 IN COMPLEX WITH DTDP-D- REMARK 900 GLUCOSE 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 1NXM A 1 197 UNP Q8GIQ0 Q8GIQ0_STRSU 1 197 DBREF 1NXM 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 FORMUL 3 HOH *633(H2 O) HELIX 1 1 LYS A 42 LEU A 46 1 5 HELIX 2 2 PRO A 51 ALA A 56 5 6 HELIX 3 3 ALA A 147 TYR A 154 5 8 HELIX 4 4 SER A 177 ASN A 182 1 6 HELIX 5 5 PHE A 185 VAL A 189 5 5 HELIX 6 6 ARG A 193 LEU A 197 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 ASN B 170 ALA B 174 5 5 HELIX 12 12 SER B 177 ASN B 182 1 6 HELIX 13 13 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 GLU A 23 N ARG A 13 SHEET 3 A 8 LYS A 117 VAL A 121 -1 O SER A 118 N PHE A 24 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 TRP B 35 N PHE A 66 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 PHE B 66 N TRP A 35 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 PHE B 24 O SER B 118 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 GLY A 94 O THR A 111 SHEET 3 C 5 VAL A 125 VAL A 131 -1 O GLN A 130 N LEU A 93 SHEET 4 C 5 LEU A 72 ALA A 77 -1 N HIS A 76 O ASN A 127 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 -0.53 CISPEP 2 GLY B 74 LEU B 75 0 -1.15 CRYST1 45.671 81.624 52.098 90.00 108.80 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 0.021895 0.000000 0.007454 0.00000 SCALE2 0.000000 0.012251 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020277 0.00000