HEADER TRANSFERASE 26-JUN-18 6GX2 TITLE BLOOD GROUP SYNTHASE AAGLYB IN COMPLEX WITH UDP-GALNAC AND TITLE 2 CRYOPROTECTED WITH GLYCEROL COMPND MOL_ID: 1; COMPND 2 MOLECULE: ABO BLOOD GROUP (TRANSFERASE A, ALPHA 1-3-N- COMPND 3 ACETYLGALACTOSAMINYLTRANSFERASE TRANSFERASE B, ALPHA 1-3- COMPND 4 GALACTOSYLTRANSFERASE); COMPND 5 CHAIN: A; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ABO; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BLOOD GROUP SYNTHASE, GLYCOSYLTRANSFERASE, DUAL SPECIFICITY, CIS-AB KEYWDS 2 MUTANT, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.ROCHA,A.ROYANT REVDAT 2 17-JAN-24 6GX2 1 LINK REVDAT 1 10-JUL-19 6GX2 0 JRNL AUTH J.ROCHA,G.O.BATOT,M.M.PALCIC,C.BRETON,A.ROYANT JRNL TITL BLOOD GROUP SYNTHASE AAGLYB IN COMPLEX WITH UDP-GALNAC AND JRNL TITL 2 CRYOPROTECTED WITH GLYCEROL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 129085 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.113 REMARK 3 R VALUE (WORKING SET) : 0.112 REMARK 3 FREE R VALUE : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6857 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) : 1.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 9276 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2180 REMARK 3 BIN FREE R VALUE SET COUNT : 504 REMARK 3 BIN FREE R VALUE : 0.2360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2435 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 413 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.11000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -0.12000 REMARK 3 B12 (A**2) : 0.00000 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): 0.023 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.024 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.016 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.725 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.984 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3016 ; 0.011 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 2646 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4140 ; 1.728 ; 1.681 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6246 ; 1.115 ; 1.644 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 382 ; 7.142 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 173 ;30.744 ;20.636 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 508 ;12.091 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;22.623 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3545 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 603 ; 0.003 ; 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): 1423 ; 1.180 ; 0.924 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1422 ; 1.178 ; 0.921 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1840 ; 1.482 ; 1.397 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1841 ; 1.483 ; 1.399 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1593 ; 1.782 ; 1.175 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1585 ; 1.754 ; 1.168 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2289 ; 2.074 ; 1.665 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3566 ; 2.842 ;12.386 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3422 ; 2.471 ;11.401 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5662 ; 2.116 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 283 ;19.222 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5730 ; 7.602 ; 5.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6GX2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1200010620. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 135972 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 49.560 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09500 REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.09 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.71000 REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 3ZGG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MOPS BUFFER, MAGNESIUM CHLORIDE, REMARK 280 AMMONIUM SULFATE AND PEG3350, PH 7, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.83850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.83850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 26.28450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 74.34100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 26.28450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 74.34100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.83850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 26.28450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 74.34100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.83850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 26.28450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 74.34100 REMARK 290 SMTRY3 8 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: 10120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -39.83850 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 783 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 825 LIES ON A SPECIAL POSITION. 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 57 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 707 O HOH A 863 2.18 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 PHE A 269 CB - CG - CD1 ANGL. DEV. = 4.5 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 GLU A 61 85.13 61.72 REMARK 500 LYS A 124 -130.54 57.95 REMARK 500 LYS A 124 -130.54 57.43 REMARK 500 ARG A 198 -91.85 -93.29 REMARK 500 ARG A 199 -47.05 -137.76 REMARK 500 THR A 245 48.10 -88.98 REMARK 500 PHE A 269 102.48 -160.61 REMARK 500 HIS A 301 -138.54 64.84 REMARK 500 HIS A 301 -123.99 41.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 282 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 910 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 911 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 912 DISTANCE = 5.95 ANGSTROMS REMARK 525 HOH A 913 DISTANCE = 7.15 ANGSTROMS 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 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 211 OD2 REMARK 620 2 ASP A 213 OD1 98.9 REMARK 620 3 ASP A 213 OD2 154.9 56.0 REMARK 620 4 UDP A 402 O1B 101.5 158.7 103.4 REMARK 620 5 UDP A 402 O1A 93.3 83.0 83.0 89.8 REMARK 620 6 HOH A 719 O 93.8 97.5 91.2 87.2 172.7 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UDP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 409 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ZGF RELATED DB: PDB REMARK 900 RELATED ID: 3ZGG RELATED DB: PDB REMARK 900 RELATED ID: 5M79 RELATED DB: PDB REMARK 900 RELATED ID: 5M7A RELATED DB: PDB REMARK 900 RELATED ID: 5M7B RELATED DB: PDB REMARK 900 RELATED ID: 5M7C RELATED DB: PDB REMARK 900 RELATED ID: 5M7D RELATED DB: PDB DBREF 6GX2 A 64 354 UNP F0X360 F0X360_HUMAN 54 344 SEQADV 6GX2 MET A 57 UNP F0X360 INITIATING METHIONINE SEQADV 6GX2 ALA A 58 UNP F0X360 EXPRESSION TAG SEQADV 6GX2 ILE A 59 UNP F0X360 EXPRESSION TAG SEQADV 6GX2 GLY A 60 UNP F0X360 EXPRESSION TAG SEQADV 6GX2 GLU A 61 UNP F0X360 EXPRESSION TAG SEQADV 6GX2 PHE A 62 UNP F0X360 EXPRESSION TAG SEQADV 6GX2 MET A 63 UNP F0X360 EXPRESSION TAG SEQADV 6GX2 GLY A 266 UNP F0X360 LEU 256 ENGINEERED MUTATION SEQRES 1 A 298 MET ALA ILE GLY GLU PHE MET VAL SER LEU PRO ARG MET SEQRES 2 A 298 VAL TYR PRO GLN PRO LYS VAL LEU THR PRO CYS ARG LYS SEQRES 3 A 298 ASP VAL LEU VAL VAL THR PRO TRP LEU ALA PRO ILE VAL SEQRES 4 A 298 TRP GLU GLY THR PHE ASN ILE ASP ILE LEU ASN GLU GLN SEQRES 5 A 298 PHE ARG LEU GLN ASN THR THR ILE GLY LEU THR VAL PHE SEQRES 6 A 298 ALA ILE LYS LYS TYR VAL ALA PHE LEU LYS LEU PHE LEU SEQRES 7 A 298 GLU THR ALA GLU LYS HIS PHE MET VAL GLY HIS ARG VAL SEQRES 8 A 298 HIS TYR TYR VAL PHE THR ASP GLN PRO ALA ALA VAL PRO SEQRES 9 A 298 ARG VAL THR LEU GLY THR GLY ARG GLN LEU SER VAL LEU SEQRES 10 A 298 GLU VAL ARG ALA TYR LYS ARG TRP GLN ASP VAL SER MET SEQRES 11 A 298 ARG ARG MET GLU MET ILE SER ASP PHE CYS GLU ARG ARG SEQRES 12 A 298 PHE LEU SER GLU VAL ASP TYR LEU VAL CYS VAL ASP VAL SEQRES 13 A 298 ASP MET GLU PHE ARG ASP HIS VAL GLY VAL GLU ILE LEU SEQRES 14 A 298 THR PRO LEU PHE GLY THR LEU HIS PRO GLY PHE TYR GLY SEQRES 15 A 298 SER SER ARG GLU ALA PHE THR TYR GLU ARG ARG PRO GLN SEQRES 16 A 298 SER GLN ALA TYR ILE PRO LYS ASP GLU GLY ASP PHE TYR SEQRES 17 A 298 TYR GLY GLY ALA PHE PHE GLY GLY SER VAL GLN GLU VAL SEQRES 18 A 298 GLN ARG LEU THR ARG ALA CYS HIS GLN ALA MET MET VAL SEQRES 19 A 298 ASP GLN ALA ASN GLY ILE GLU ALA VAL TRP HIS ASP GLU SEQRES 20 A 298 SER HIS LEU ASN LYS TYR LEU LEU ARG HIS LYS PRO THR SEQRES 21 A 298 LYS VAL LEU SER PRO GLU TYR LEU TRP ASP GLN GLN LEU SEQRES 22 A 298 LEU GLY TRP PRO ALA VAL LEU ARG LYS LEU ARG PHE THR SEQRES 23 A 298 ALA VAL PRO LYS ASN HIS GLN ALA VAL ARG ASN PRO HET MN A 401 1 HET UDP A 402 25 HET GOL A 403 6 HET GOL A 404 6 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET SO4 A 408 5 HET SO4 A 409 5 HETNAM MN MANGANESE (II) ION HETNAM UDP URIDINE-5'-DIPHOSPHATE HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MN MN 2+ FORMUL 3 UDP C9 H14 N2 O12 P2 FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 EDO 3(C2 H6 O2) FORMUL 9 SO4 2(O4 S 2-) FORMUL 11 HOH *413(H2 O) HELIX 1 AA1 ASN A 101 GLN A 112 1 12 HELIX 2 AA2 ILE A 123 ALA A 128 5 6 HELIX 3 AA3 PHE A 129 PHE A 141 1 13 HELIX 4 AA4 GLN A 155 VAL A 159 5 5 HELIX 5 AA5 ARG A 180 ARG A 199 1 20 HELIX 6 AA6 ARG A 199 VAL A 204 1 6 HELIX 7 AA7 GLY A 221 LEU A 225 5 5 HELIX 8 AA8 SER A 240 PHE A 244 5 5 HELIX 9 AA9 VAL A 274 ASN A 294 1 21 HELIX 10 AB1 TRP A 300 HIS A 313 1 14 HELIX 11 AB2 PRO A 321 LEU A 324 5 4 HELIX 12 AB3 ASP A 326 GLY A 331 1 6 HELIX 13 AB4 ASN A 347 ARG A 352 1 6 SHEET 1 AA1 8 ILE A 94 VAL A 95 0 SHEET 2 AA1 8 LYS A 317 LEU A 319 1 O VAL A 318 N VAL A 95 SHEET 3 AA1 8 LEU A 228 THR A 231 1 N GLY A 230 O LEU A 319 SHEET 4 AA1 8 PHE A 269 SER A 273 -1 O GLY A 271 N PHE A 229 SHEET 5 AA1 8 TYR A 206 VAL A 210 -1 N CYS A 209 O PHE A 270 SHEET 6 AA1 8 THR A 115 ALA A 122 1 N GLY A 117 O TYR A 206 SHEET 7 AA1 8 ARG A 146 THR A 153 1 O PHE A 152 N ALA A 122 SHEET 8 AA1 8 ARG A 168 GLU A 174 1 O GLN A 169 N TYR A 149 SHEET 1 AA2 2 MET A 214 PHE A 216 0 SHEET 2 AA2 2 PHE A 341 ALA A 343 -1 O THR A 342 N GLU A 215 LINK OD2 ASP A 211 MN MN A 401 1555 1555 2.09 LINK OD1 ASP A 213 MN MN A 401 1555 1555 2.23 LINK OD2 ASP A 213 MN MN A 401 1555 1555 2.41 LINK MN MN A 401 O1B UDP A 402 1555 1555 2.06 LINK MN MN A 401 O1A UDP A 402 1555 1555 2.18 LINK MN MN A 401 O HOH A 719 1555 1555 2.18 SITE 1 AC1 4 ASP A 211 ASP A 213 UDP A 402 HOH A 719 SITE 1 AC2 20 PHE A 121 ILE A 123 TYR A 126 VAL A 184 SITE 2 AC2 20 ARG A 188 ASP A 211 VAL A 212 ASP A 213 SITE 3 AC2 20 LYS A 346 HIS A 348 ARG A 352 MN A 401 SITE 4 AC2 20 GOL A 404 HOH A 503 HOH A 522 HOH A 533 SITE 5 AC2 20 HOH A 572 HOH A 578 HOH A 614 HOH A 719 SITE 1 AC3 9 HIS A 233 PHE A 236 THR A 245 TRP A 300 SITE 2 AC3 9 GLU A 303 HOH A 565 HOH A 568 HOH A 577 SITE 3 AC3 9 HOH A 578 SITE 1 AC4 13 ARG A 188 ASP A 211 GLY A 267 ALA A 268 SITE 2 AC4 13 TRP A 300 HIS A 301 ASP A 302 GLU A 303 SITE 3 AC4 13 UDP A 402 HOH A 503 HOH A 676 HOH A 680 SITE 4 AC4 13 HOH A 762 SITE 1 AC5 11 MET A 69 TYR A 71 ARG A 241 GLU A 260 SITE 2 AC5 11 GLY A 261 ASP A 262 LEU A 311 HOH A 624 SITE 3 AC5 11 HOH A 678 HOH A 740 HOH A 751 SITE 1 AC6 8 TYR A 71 PRO A 72 PRO A 89 ASN A 101 SITE 2 AC6 8 HOH A 511 HOH A 741 HOH A 796 HOH A 827 SITE 1 AC7 4 VAL A 70 TYR A 71 PRO A 72 ARG A 241 SITE 1 AC8 7 ARG A 110 ASN A 113 ARG A 146 THR A 166 SITE 2 AC8 7 GLY A 167 HOH A 517 HOH A 714 SITE 1 AC9 4 ARG A 176 TYR A 178 LYS A 179 HOH A 505 CRYST1 52.569 148.682 79.677 90.00 90.00 90.00 C 2 2 21 8 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 0.019023 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006726 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012551 0.00000