HEADER TRANSFERASE 08-APR-05 2BO6 TITLE DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL TITLE 2 MANNOSYLTRANSFERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MANNOSYLGLYCERATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 2.4.1.-; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOTHERMUS MARINUS; SOURCE 3 ORGANISM_TAXID: 29549; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: TUNER; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET22B KEYWDS CATALYSIS, GLYCOSYLTRANSFERASE, MANNOSE, TRANSFERASE, KEYWDS 2 STEREOSELECTIVITY EXPDTA X-RAY DIFFRACTION AUTHOR J.FLINT,E.TAYLOR,M.YANG,D.N.BOLAM,L.E.TAILFORD,C.MARTINEZ-FLEITES, AUTHOR 2 E.J.DODSON,B.G.DAVIS,H.J.GILBERT,G.J.DAVIES REVDAT 5 08-MAY-24 2BO6 1 LINK REVDAT 4 13-JUL-11 2BO6 1 VERSN REVDAT 3 24-FEB-09 2BO6 1 VERSN REVDAT 2 20-DEC-06 2BO6 1 JRNL REVDAT 1 06-JUN-05 2BO6 0 JRNL AUTH J.FLINT,E.TAYLOR,M.YANG,D.N.BOLAM,L.E.TAILFORD, JRNL AUTH 2 C.MARTINEZ-FLEITES,E.J.DODSON,B.G.DAVIS,H.J.GILBERT, JRNL AUTH 3 G.J.DAVIES JRNL TITL STRUCTURAL DISSECTION AND HIGH-THROUGHPUT SCREENING OF JRNL TITL 2 MANNOSYLGLYCEERATE SYNTHASE JRNL REF NAT.STRUCT.MOL.BIOL. V. 12 608 2005 JRNL REFN ISSN 1545-9993 JRNL PMID 15951819 JRNL DOI 10.1038/NSMB950 REMARK 2 REMARK 2 RESOLUTION. 2.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 2.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 69404 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) : 0.255 REMARK 3 R VALUE (WORKING SET) : 0.253 REMARK 3 FREE R VALUE : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3694 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) : 2.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5063 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3640 REMARK 3 BIN FREE R VALUE SET COUNT : 277 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6276 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 100 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -0.20000 REMARK 3 B33 (A**2) : 0.29000 REMARK 3 B12 (A**2) : -0.10000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.242 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.211 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.225 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.780 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.911 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6470 ; 0.018 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 5810 ; 0.009 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8800 ; 1.367 ; 1.930 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13372 ; 0.887 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 758 ; 5.795 ; 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): 932 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7232 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1482 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1424 ; 0.207 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 6709 ; 0.222 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 3550 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 131 ; 0.174 ; 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): 52 ; 0.318 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 93 ; 0.264 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 6 ; 0.286 ; 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): 3792 ; 0.393 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6128 ; 0.636 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2678 ; 1.302 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2672 ; 1.977 ; 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 : NULL 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 2 A 382 REMARK 3 ORIGIN FOR THE GROUP (A): -12.3791 66.4108 36.5874 REMARK 3 T TENSOR REMARK 3 T11: 0.1285 T22: 0.6213 REMARK 3 T33: 0.2633 T12: -0.2822 REMARK 3 T13: -0.0066 T23: 0.0351 REMARK 3 L TENSOR REMARK 3 L11: 2.1812 L22: 1.5054 REMARK 3 L33: 3.3182 L12: -0.2380 REMARK 3 L13: 0.5371 L23: 1.0824 REMARK 3 S TENSOR REMARK 3 S11: 0.3976 S12: -0.4163 S13: -0.2590 REMARK 3 S21: 0.1470 S22: -0.2615 S23: 0.0501 REMARK 3 S31: 0.7469 S32: -0.6896 S33: -0.1361 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 2 B 382 REMARK 3 ORIGIN FOR THE GROUP (A): -35.1314 79.4784 76.5553 REMARK 3 T TENSOR REMARK 3 T11: 0.2300 T22: 0.5450 REMARK 3 T33: 0.2789 T12: -0.1712 REMARK 3 T13: 0.0523 T23: 0.0823 REMARK 3 L TENSOR REMARK 3 L11: 3.5099 L22: 2.8266 REMARK 3 L33: 2.2091 L12: 1.6591 REMARK 3 L13: -1.2683 L23: -0.4624 REMARK 3 S TENSOR REMARK 3 S11: -0.3108 S12: 0.9771 S13: 0.3858 REMARK 3 S21: 0.0423 S22: 0.6199 S23: 0.5544 REMARK 3 S31: -0.1041 S32: -0.8420 S33: -0.3091 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 2BO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-APR-05. REMARK 100 THE DEPOSITION ID IS D_1290023571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9783 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL REMARK 200 DATA SCALING SOFTWARE : HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74145 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 36.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 80.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 6.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M TRI-SODIUM CITRATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE, PH 4.6, 30% (V/V) MPD REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 102.85667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.42833 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.42833 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 102.85667 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PQS 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 102.85667 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 GLY A 383 REMARK 465 ARG A 384 REMARK 465 GLY A 385 REMARK 465 HIS A 386 REMARK 465 PRO A 387 REMARK 465 VAL A 388 REMARK 465 PRO A 389 REMARK 465 PRO A 390 REMARK 465 ARG A 391 REMARK 465 ALA A 392 REMARK 465 ALA A 393 REMARK 465 LEU A 394 REMARK 465 SER A 395 REMARK 465 THR A 396 REMARK 465 ALA A 397 REMARK 465 MET B 1 REMARK 465 GLY B 383 REMARK 465 ARG B 384 REMARK 465 GLY B 385 REMARK 465 HIS B 386 REMARK 465 PRO B 387 REMARK 465 VAL B 388 REMARK 465 PRO B 389 REMARK 465 PRO B 390 REMARK 465 ARG B 391 REMARK 465 ALA B 392 REMARK 465 ALA B 393 REMARK 465 LEU B 394 REMARK 465 SER B 395 REMARK 465 THR B 396 REMARK 465 ALA B 397 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 382 CA C O CB CG OD1 ND2 REMARK 470 ASN B 382 CA C O CB CG OD1 ND2 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 HIS A 18 O HOH A 2004 2.11 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 OE1 GLN A 330 OE2 GLU B 288 2664 2.17 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 GLU A 254 CD GLU A 254 OE1 0.165 REMARK 500 ASP A 333 CG ASP A 333 OD2 0.225 REMARK 500 GLY A 359 C GLY A 359 O 0.102 REMARK 500 GLU B 254 CG GLU B 254 CD 0.158 REMARK 500 GLU B 288 CD GLU B 288 OE2 0.111 REMARK 500 ASN B 311 CB ASN B 311 CG 0.142 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 ARG A 68 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 144 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 182 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ASP A 333 CB - CG - OD1 ANGL. DEV. = -11.1 DEGREES REMARK 500 ASP A 333 CB - CG - OD2 ANGL. DEV. = 8.2 DEGREES REMARK 500 ASP B 40 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP B 119 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP B 224 CB - CG - OD2 ANGL. DEV. = 6.5 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 9 -116.10 -131.81 REMARK 500 HIS A 10 64.19 -101.49 REMARK 500 GLN A 92 33.28 -144.33 REMARK 500 PHE A 120 -34.60 -32.97 REMARK 500 ILE A 142 -55.67 -122.37 REMARK 500 ASP A 188 -160.55 -100.35 REMARK 500 LEU A 223 -23.47 -27.48 REMARK 500 ASP A 224 -39.63 -37.37 REMARK 500 ALA A 249 106.67 177.50 REMARK 500 GLN A 253 118.75 -164.59 REMARK 500 PHE A 310 -3.69 -160.87 REMARK 500 MET A 313 58.21 -91.67 REMARK 500 ASP A 314 -170.05 -69.50 REMARK 500 VAL A 355 -57.57 -132.08 REMARK 500 LEU A 380 37.81 -87.61 REMARK 500 GLU A 381 37.60 -154.26 REMARK 500 LYS B 9 -85.12 -153.50 REMARK 500 ARG B 39 53.96 -90.86 REMARK 500 LEU B 72 -159.20 -97.15 REMARK 500 ILE B 103 104.51 -54.77 REMARK 500 ASP B 188 -151.09 -107.68 REMARK 500 LYS B 215 149.07 -179.33 REMARK 500 HIS B 217 102.95 -44.49 REMARK 500 TYR B 220 96.89 -66.94 REMARK 500 ALA B 249 117.52 175.37 REMARK 500 GLU B 254 128.55 -27.22 REMARK 500 GLU B 265 34.57 -95.26 REMARK 500 PHE B 310 -16.92 -161.41 REMARK 500 VAL B 355 -60.66 -121.91 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 MN A1383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B1383 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGY A1382 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DGY B1382 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BO4 RELATED DB: PDB REMARK 900 DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL REMARK 900 MANNOSYLTRANSFERASE REMARK 900 RELATED ID: 2BO7 RELATED DB: PDB REMARK 900 DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL REMARK 900 MANNOSYLTRANSFERASE REMARK 900 RELATED ID: 2BO8 RELATED DB: PDB REMARK 900 DISSECTION OF MANNOSYLGLYCERATE SYNTHASE: AN ARCHETYPAL REMARK 900 MANNOSYLTRANSFERASE DBREF 2BO6 A 1 397 UNP Q9RFR0 Q9RFR0_RHOMR 1 397 DBREF 2BO6 B 1 397 UNP Q9RFR0 Q9RFR0_RHOMR 1 397 SEQRES 1 A 397 MET SER LEU VAL VAL PHE PRO PHE LYS HIS GLU HIS PRO SEQRES 2 A 397 GLU VAL LEU LEU HIS ASN VAL ARG VAL ALA ALA ALA HIS SEQRES 3 A 397 PRO ARG VAL HIS GLU VAL LEU CYS ILE GLY TYR GLU ARG SEQRES 4 A 397 ASP GLN THR TYR GLU ALA VAL GLU ARG ALA ALA PRO GLU SEQRES 5 A 397 ILE SER ARG ALA THR GLY THR PRO VAL SER VAL ARG LEU SEQRES 6 A 397 GLN GLU ARG LEU GLY THR LEU ARG PRO GLY LYS GLY ASP SEQRES 7 A 397 GLY MET ASN THR ALA LEU ARG TYR PHE LEU GLU GLU THR SEQRES 8 A 397 GLN TRP GLU ARG ILE HIS PHE TYR ASP ALA ASP ILE THR SEQRES 9 A 397 SER PHE GLY PRO ASP TRP ILE THR LYS ALA GLU GLU ALA SEQRES 10 A 397 ALA ASP PHE GLY TYR GLY LEU VAL ARG HIS TYR PHE PRO SEQRES 11 A 397 ARG ALA SER THR ASP ALA MET ILE THR TRP MET ILE THR SEQRES 12 A 397 ARG THR GLY PHE ALA LEU LEU TRP PRO HIS THR GLU LEU SEQRES 13 A 397 SER TRP ILE GLU GLN PRO LEU GLY GLY GLU LEU LEU MET SEQRES 14 A 397 ARG ARG GLU VAL ALA ALA MET LEU TYR GLU ASP GLU ARG SEQRES 15 A 397 VAL ARG ARG ARG SER ASP TRP GLY ILE ASP THR LEU TYR SEQRES 16 A 397 THR PHE VAL THR VAL GLN GLN GLY VAL SER ILE TYR GLU SEQRES 17 A 397 CYS TYR ILE PRO GLU GLY LYS ALA HIS ARG LEU TYR GLY SEQRES 18 A 397 GLY LEU ASP ASP LEU ARG THR MET LEU VAL GLU CYS PHE SEQRES 19 A 397 ALA ALA ILE GLN SER LEU GLN HIS GLU VAL VAL GLY GLN SEQRES 20 A 397 PRO ALA ILE HIS ARG GLN GLU HIS PRO HIS ARG VAL PRO SEQRES 21 A 397 VAL HIS ILE ALA GLU ARG VAL GLY TYR ASP VAL GLU ALA SEQRES 22 A 397 THR LEU HIS ARG LEU MET GLN HIS TRP THR PRO ARG GLN SEQRES 23 A 397 VAL GLU LEU LEU GLU LEU PHE THR THR PRO VAL ARG GLU SEQRES 24 A 397 GLY LEU ARG THR CYS GLN ARG ARG PRO ALA PHE ASN PHE SEQRES 25 A 397 MET ASP GLU MET ALA TRP ALA ALA THR TYR HIS VAL LEU SEQRES 26 A 397 LEU GLU HIS PHE GLN PRO GLY ASP PRO ASP TRP GLU GLU SEQRES 27 A 397 LEU LEU PHE LYS LEU TRP THR THR ARG VAL LEU ASN TYR SEQRES 28 A 397 THR MET THR VAL ALA LEU ARG GLY TYR ASP TYR ALA GLN SEQRES 29 A 397 GLN TYR LEU TYR ARG MET LEU GLY ARG TYR ARG TYR GLN SEQRES 30 A 397 ALA ALA LEU GLU ASN GLY ARG GLY HIS PRO VAL PRO PRO SEQRES 31 A 397 ARG ALA ALA LEU SER THR ALA SEQRES 1 B 397 MET SER LEU VAL VAL PHE PRO PHE LYS HIS GLU HIS PRO SEQRES 2 B 397 GLU VAL LEU LEU HIS ASN VAL ARG VAL ALA ALA ALA HIS SEQRES 3 B 397 PRO ARG VAL HIS GLU VAL LEU CYS ILE GLY TYR GLU ARG SEQRES 4 B 397 ASP GLN THR TYR GLU ALA VAL GLU ARG ALA ALA PRO GLU SEQRES 5 B 397 ILE SER ARG ALA THR GLY THR PRO VAL SER VAL ARG LEU SEQRES 6 B 397 GLN GLU ARG LEU GLY THR LEU ARG PRO GLY LYS GLY ASP SEQRES 7 B 397 GLY MET ASN THR ALA LEU ARG TYR PHE LEU GLU GLU THR SEQRES 8 B 397 GLN TRP GLU ARG ILE HIS PHE TYR ASP ALA ASP ILE THR SEQRES 9 B 397 SER PHE GLY PRO ASP TRP ILE THR LYS ALA GLU GLU ALA SEQRES 10 B 397 ALA ASP PHE GLY TYR GLY LEU VAL ARG HIS TYR PHE PRO SEQRES 11 B 397 ARG ALA SER THR ASP ALA MET ILE THR TRP MET ILE THR SEQRES 12 B 397 ARG THR GLY PHE ALA LEU LEU TRP PRO HIS THR GLU LEU SEQRES 13 B 397 SER TRP ILE GLU GLN PRO LEU GLY GLY GLU LEU LEU MET SEQRES 14 B 397 ARG ARG GLU VAL ALA ALA MET LEU TYR GLU ASP GLU ARG SEQRES 15 B 397 VAL ARG ARG ARG SER ASP TRP GLY ILE ASP THR LEU TYR SEQRES 16 B 397 THR PHE VAL THR VAL GLN GLN GLY VAL SER ILE TYR GLU SEQRES 17 B 397 CYS TYR ILE PRO GLU GLY LYS ALA HIS ARG LEU TYR GLY SEQRES 18 B 397 GLY LEU ASP ASP LEU ARG THR MET LEU VAL GLU CYS PHE SEQRES 19 B 397 ALA ALA ILE GLN SER LEU GLN HIS GLU VAL VAL GLY GLN SEQRES 20 B 397 PRO ALA ILE HIS ARG GLN GLU HIS PRO HIS ARG VAL PRO SEQRES 21 B 397 VAL HIS ILE ALA GLU ARG VAL GLY TYR ASP VAL GLU ALA SEQRES 22 B 397 THR LEU HIS ARG LEU MET GLN HIS TRP THR PRO ARG GLN SEQRES 23 B 397 VAL GLU LEU LEU GLU LEU PHE THR THR PRO VAL ARG GLU SEQRES 24 B 397 GLY LEU ARG THR CYS GLN ARG ARG PRO ALA PHE ASN PHE SEQRES 25 B 397 MET ASP GLU MET ALA TRP ALA ALA THR TYR HIS VAL LEU SEQRES 26 B 397 LEU GLU HIS PHE GLN PRO GLY ASP PRO ASP TRP GLU GLU SEQRES 27 B 397 LEU LEU PHE LYS LEU TRP THR THR ARG VAL LEU ASN TYR SEQRES 28 B 397 THR MET THR VAL ALA LEU ARG GLY TYR ASP TYR ALA GLN SEQRES 29 B 397 GLN TYR LEU TYR ARG MET LEU GLY ARG TYR ARG TYR GLN SEQRES 30 B 397 ALA ALA LEU GLU ASN GLY ARG GLY HIS PRO VAL PRO PRO SEQRES 31 B 397 ARG ALA ALA LEU SER THR ALA HET DGY A1382 7 HET MN A1383 1 HET DGY B1382 7 HET MN B1383 1 HETNAM DGY (2R)-2,3-DIHYDROXYPROPANOIC ACID HETNAM MN MANGANESE (II) ION FORMUL 3 DGY 2(C3 H6 O4) FORMUL 4 MN 2(MN 2+) FORMUL 7 HOH *100(H2 O) HELIX 1 1 HIS A 12 HIS A 26 1 15 HELIX 2 2 ASP A 40 GLY A 58 1 19 HELIX 3 3 GLY A 75 GLU A 90 1 16 HELIX 4 4 GLY A 107 PHE A 120 1 14 HELIX 5 5 ALA A 136 ILE A 142 1 7 HELIX 6 6 ILE A 142 TRP A 151 1 10 HELIX 7 7 GLU A 155 ILE A 159 5 5 HELIX 8 8 ARG A 171 ASP A 180 1 10 HELIX 9 9 ASP A 180 ARG A 186 1 7 HELIX 10 10 GLY A 190 GLN A 202 1 13 HELIX 11 11 GLY A 222 ASP A 225 5 4 HELIX 12 12 LEU A 226 GLN A 241 1 16 HELIX 13 13 PRO A 260 GLU A 265 1 6 HELIX 14 14 ASP A 270 LEU A 278 1 9 HELIX 15 15 THR A 283 LEU A 290 1 8 HELIX 16 16 GLU A 291 PHE A 293 5 3 HELIX 17 17 THR A 294 CYS A 304 1 11 HELIX 18 18 ASP A 314 PHE A 329 1 16 HELIX 19 19 ASP A 333 VAL A 355 1 23 HELIX 20 20 ALA A 356 ARG A 358 5 3 HELIX 21 21 GLY A 359 LEU A 380 1 22 HELIX 22 22 HIS B 12 HIS B 26 1 15 HELIX 23 23 ASP B 40 THR B 57 1 18 HELIX 24 24 GLY B 75 GLU B 90 1 16 HELIX 25 25 GLY B 107 ALA B 118 1 12 HELIX 26 26 ALA B 136 ILE B 142 1 7 HELIX 27 27 ILE B 142 TRP B 151 1 10 HELIX 28 28 GLU B 155 ILE B 159 5 5 HELIX 29 29 ARG B 171 ASP B 180 1 10 HELIX 30 30 ASP B 180 ARG B 185 1 6 HELIX 31 31 GLY B 190 GLN B 202 1 13 HELIX 32 32 GLY B 222 ASP B 225 5 4 HELIX 33 33 LEU B 226 LEU B 240 1 15 HELIX 34 34 PRO B 260 GLU B 265 1 6 HELIX 35 35 ASP B 270 MET B 279 1 10 HELIX 36 36 THR B 283 LEU B 290 1 8 HELIX 37 37 GLU B 291 PHE B 293 5 3 HELIX 38 38 THR B 294 CYS B 304 1 11 HELIX 39 39 ASP B 314 PHE B 329 1 16 HELIX 40 40 ASP B 333 VAL B 355 1 23 HELIX 41 41 ALA B 356 ARG B 358 5 3 HELIX 42 42 GLY B 359 GLU B 381 1 23 SHEET 1 AA 8 VAL A 61 LEU A 65 0 SHEET 2 AA 8 GLU A 31 GLY A 36 1 O VAL A 32 N SER A 62 SHEET 3 AA 8 LEU A 3 PRO A 7 1 O VAL A 4 N LEU A 33 SHEET 4 AA 8 ARG A 95 PHE A 98 1 O ARG A 95 N LEU A 3 SHEET 5 AA 8 LEU A 167 ARG A 170 -1 O LEU A 167 N PHE A 98 SHEET 6 AA 8 LEU A 124 TYR A 128 -1 O VAL A 125 N LEU A 168 SHEET 7 AA 8 ILE A 206 TYR A 210 1 O TYR A 207 N ARG A 126 SHEET 8 AA 8 HIS A 251 GLN A 253 1 O ARG A 252 N GLU A 208 SHEET 1 BA 8 VAL B 61 LEU B 65 0 SHEET 2 BA 8 GLU B 31 GLY B 36 1 O VAL B 32 N SER B 62 SHEET 3 BA 8 LEU B 3 PHE B 8 1 O VAL B 4 N LEU B 33 SHEET 4 BA 8 ARG B 95 PHE B 98 1 O ARG B 95 N LEU B 3 SHEET 5 BA 8 LEU B 167 ARG B 170 -1 O LEU B 167 N PHE B 98 SHEET 6 BA 8 LEU B 124 TYR B 128 -1 O VAL B 125 N LEU B 168 SHEET 7 BA 8 ILE B 206 TYR B 210 1 O TYR B 207 N ARG B 126 SHEET 8 BA 8 HIS B 251 GLN B 253 1 O ARG B 252 N GLU B 208 LINK OD2 ASP A 102 MN MN A1383 1555 1555 2.18 LINK OD2 ASP B 102 MN MN B1383 1555 1555 2.11 SITE 1 AC1 1 ASP A 102 SITE 1 AC2 2 ASP B 100 ASP B 102 SITE 1 AC3 6 ARG A 131 ALA A 136 MET A 137 ILE A 138 SITE 2 AC3 6 THR A 139 MET A 229 SITE 1 AC4 6 ARG B 131 ALA B 136 MET B 137 ILE B 138 SITE 2 AC4 6 THR B 139 HOH B2053 CRYST1 150.228 150.228 154.285 90.00 90.00 120.00 P 32 2 1 12 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 0.006657 0.003843 0.000000 0.00000 SCALE2 0.000000 0.007686 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006482 0.00000