HEADER TRANSFERASE 17-APR-15 5A07 TITLE X-RAY STRUCTURE OF THE MANNOSYLTRANSFERASE KTR4P FROM S. CEREVISIAE IN TITLE 2 COMPLEX WITH GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE MANNOSYLTRANSFERASE KTR4; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: LUMENAL PART, RESIDUES 33-464; COMPND 5 SYNONYM: KTR4P; COMPND 6 EC: 2.4.1.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: S288C; SOURCE 6 ATCC: 204508; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: K-12; SOURCE 10 EXPRESSION_SYSTEM_VARIANT: ROSETTA-GAMI 2; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PNIC28-BSA4 KEYWDS TRANSFERASE, GOLGI APPARATUS, MANNOSYLTRANSFERASES, GT-A, MEMBRANE KEYWDS 2 PROTEINS EXPDTA X-RAY DIFFRACTION AUTHOR D.D.D.POSSNER,J.E.GUY REVDAT 3 10-JAN-24 5A07 1 REMARK LINK REVDAT 2 02-SEP-15 5A07 1 JRNL REVDAT 1 26-AUG-15 5A07 0 JRNL AUTH D.D.D.POSSNER,M.CLAESSON,J.E.GUY JRNL TITL STRUCTURE OF THE GLYCOSYLTRANSFERASE KTR4P FROM JRNL TITL 2 SACCHAROMYCES CEREVISIAE JRNL REF PLOS ONE V. 10 36239 2015 JRNL REFN ESSN 1932-6203 JRNL PMID 26296208 JRNL DOI 10.1371/JOURNAL.PONE.013623 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 86.79 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 76662 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3941 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5551 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2730 REMARK 3 BIN FREE R VALUE SET COUNT : 277 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6606 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 578 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.59000 REMARK 3 B22 (A**2) : -1.67000 REMARK 3 B33 (A**2) : -0.92000 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): 0.118 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.114 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.919 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.950 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6901 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6027 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9391 ; 1.828 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13947 ; 1.258 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 795 ; 6.294 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 395 ;35.192 ;25.038 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1129 ;13.760 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;19.235 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 937 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7914 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1686 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2143 ; 0.276 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 6155 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3457 ; 0.196 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 3289 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 193 ; 0.132 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.037 ; 0.200 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): 28 ; 0.388 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 26 ; 0.183 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.121 ; 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): 3167 ; 2.386 ; 2.379 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3164 ; 2.385 ; 2.379 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3956 ; 3.111 ; 3.553 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3734 ; 3.818 ; 2.756 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 5432 ; 5.823 ; 3.972 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 B 71 463 A 71 463 23881 0.10 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 5A07 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-APR-15. REMARK 100 THE DEPOSITION ID IS D_1290063623. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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) : 0.972422 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : TOROIDAL MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PIXEL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 81509 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.20 REMARK 200 R MERGE FOR SHELL (I) : 0.87000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 5A08 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA-CACODYLATE, PH 6.5 0.2M CAOAC REMARK 280 18% (W/V) PEG8000 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 30.60750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 81.32550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.31050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 81.32550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 30.60750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.31050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 31 REMARK 465 MET A 32 REMARK 465 ASN A 33 REMARK 465 GLU A 34 REMARK 465 ASN A 35 REMARK 465 TYR A 36 REMARK 465 LEU A 37 REMARK 465 GLN A 38 REMARK 465 ALA A 39 REMARK 465 VAL A 40 REMARK 465 LYS A 41 REMARK 465 ASP A 42 REMARK 465 SER A 43 REMARK 465 ALA A 44 REMARK 465 LYS A 45 REMARK 465 SER A 46 REMARK 465 GLN A 47 REMARK 465 TYR A 48 REMARK 465 ALA A 49 REMARK 465 SER A 50 REMARK 465 LEU A 51 REMARK 465 ARG A 52 REMARK 465 GLU A 53 REMARK 465 SER A 54 REMARK 465 TYR A 55 REMARK 465 LYS A 56 REMARK 465 SER A 57 REMARK 465 ILE A 58 REMARK 465 THR A 59 REMARK 465 GLY A 60 REMARK 465 LYS A 61 REMARK 465 THR A 62 REMARK 465 GLU A 63 REMARK 465 SER A 64 REMARK 465 ALA A 65 REMARK 465 ASP A 66 REMARK 465 GLU A 67 REMARK 465 LEU A 68 REMARK 465 PRO A 69 REMARK 465 SER B 31 REMARK 465 MET B 32 REMARK 465 ASN B 33 REMARK 465 GLU B 34 REMARK 465 ASN B 35 REMARK 465 TYR B 36 REMARK 465 LEU B 37 REMARK 465 GLN B 38 REMARK 465 ALA B 39 REMARK 465 VAL B 40 REMARK 465 LYS B 41 REMARK 465 ASP B 42 REMARK 465 SER B 43 REMARK 465 ALA B 44 REMARK 465 LYS B 45 REMARK 465 SER B 46 REMARK 465 GLN B 47 REMARK 465 TYR B 48 REMARK 465 ALA B 49 REMARK 465 SER B 50 REMARK 465 LEU B 51 REMARK 465 ARG B 52 REMARK 465 GLU B 53 REMARK 465 SER B 54 REMARK 465 TYR B 55 REMARK 465 LYS B 56 REMARK 465 SER B 57 REMARK 465 ILE B 58 REMARK 465 THR B 59 REMARK 465 GLY B 60 REMARK 465 LYS B 61 REMARK 465 THR B 62 REMARK 465 GLU B 63 REMARK 465 SER B 64 REMARK 465 ALA B 65 REMARK 465 ASP B 66 REMARK 465 GLU B 67 REMARK 465 LEU B 68 REMARK 465 PRO B 69 REMARK 465 ASP B 70 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 2130 O HOH A 2131 1.84 REMARK 500 OE2 GLU B 231 O HOH B 2151 1.89 REMARK 500 O HOH A 2068 O HOH A 2131 1.95 REMARK 500 O HOH A 2127 O HOH A 2131 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 SER A 361 CB SER A 361 OG 0.089 REMARK 500 SER B 115 CB SER B 115 OG -0.080 REMARK 500 GLU B 459 CG GLU B 459 CD 0.093 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 B 211 CB - CG - OD1 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 SER A 115 -68.38 -131.30 REMARK 500 TYR A 160 -63.58 -146.68 REMARK 500 PHE A 164 -33.54 -130.09 REMARK 500 TRP A 204 -52.17 -131.93 REMARK 500 GLU A 380 -160.48 -122.19 REMARK 500 ASP B 72 130.68 -37.65 REMARK 500 SER B 115 -68.41 -135.41 REMARK 500 TYR B 160 -67.08 -145.34 REMARK 500 TRP B 204 -52.47 -130.10 REMARK 500 GLU B 380 -156.28 -122.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 262 OE1 REMARK 620 2 HIS A 411 NE2 96.9 REMARK 620 3 GDP A 500 O2A 94.3 168.7 REMARK 620 4 GDP A 500 O1B 96.6 92.0 85.4 REMARK 620 5 HOH A2177 O 96.6 93.1 86.9 165.2 REMARK 620 6 HOH A2258 O 179.2 82.6 86.2 84.2 82.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 262 OE1 REMARK 620 2 HIS B 411 NE2 94.7 REMARK 620 3 GDP B 500 O3B 94.2 94.4 REMARK 620 4 GDP B 500 O2A 95.2 170.1 83.9 REMARK 620 5 HOH B2171 O 95.4 91.7 168.2 88.3 REMARK 620 6 HOH B2243 O 177.6 84.4 88.1 85.7 82.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GDP B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 1465 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 1465 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A08 RELATED DB: PDB REMARK 900 X-RAY STRUCTURE OF THE MANNOSYLTRANSFERASE KTR4P FROM S. CEREVISIAE DBREF 5A07 A 33 464 UNP P38131 KTR4_YEAST 33 464 DBREF 5A07 B 33 464 UNP P38131 KTR4_YEAST 33 464 SEQADV 5A07 SER A 31 UNP P38131 EXPRESSION TAG SEQADV 5A07 MET A 32 UNP P38131 EXPRESSION TAG SEQADV 5A07 SER B 31 UNP P38131 EXPRESSION TAG SEQADV 5A07 MET B 32 UNP P38131 EXPRESSION TAG SEQRES 1 A 434 SER MET ASN GLU ASN TYR LEU GLN ALA VAL LYS ASP SER SEQRES 2 A 434 ALA LYS SER GLN TYR ALA SER LEU ARG GLU SER TYR LYS SEQRES 3 A 434 SER ILE THR GLY LYS THR GLU SER ALA ASP GLU LEU PRO SEQRES 4 A 434 ASP HIS ASP ALA GLU VAL LEU ASP SER ILE MET ASP ARG SEQRES 5 A 434 LEU HIS GLU PRO LEU TYR GLU LYS ASP THR PHE ASP PRO SEQRES 6 A 434 ASN GLU VAL LEU ALA GLU ASN LYS GLN LEU TYR GLU GLU SEQRES 7 A 434 PHE LEU LEU GLN GLU ILE SER GLU PRO LYS VAL ASP ASN SEQRES 8 A 434 LEU VAL ARG SER GLY ASP PRO LEU ALA GLY LYS ALA LYS SEQRES 9 A 434 GLY THR ILE LEU SER LEU VAL ARG ASN SER ASP LEU GLU SEQRES 10 A 434 ASP ILE ILE SER SER ILE GLN GLN LEU GLU GLU GLU TYR SEQRES 11 A 434 ASN LYS ASN PHE GLY TYR PRO TYR THR PHE LEU ASN ASP SEQRES 12 A 434 GLU GLU PHE THR ASP GLU PHE LYS ASP GLY ILE LYS SER SEQRES 13 A 434 ILE LEU PRO LYS ASP ARG VAL VAL GLU PHE GLY THR ILE SEQRES 14 A 434 GLY PRO ASP ASN TRP ASN MET PRO ASP SER ILE ASP ARG SEQRES 15 A 434 GLU ARG TYR ASP GLN GLU MET ASP LYS MET SER LYS GLU SEQRES 16 A 434 ASN ILE GLN TYR ALA GLU VAL GLU SER TYR HIS ASN MET SEQRES 17 A 434 CYS ARG PHE TYR SER LYS GLU PHE TYR HIS HIS PRO LEU SEQRES 18 A 434 LEU SER LYS TYR LYS TYR VAL TRP ARG LEU GLU PRO ASN SEQRES 19 A 434 VAL ASN PHE TYR CYS LYS ILE ASN TYR ASP VAL PHE GLN SEQRES 20 A 434 PHE MET ASN LYS ASN ASP LYS ILE TYR GLY PHE VAL LEU SEQRES 21 A 434 ASN LEU TYR ASP SER PRO GLN THR ILE GLU THR LEU TRP SEQRES 22 A 434 THR SER THR MET ASP PHE VAL GLU GLU HIS PRO ASN TYR SEQRES 23 A 434 LEU ASN VAL ASN GLY ALA PHE ALA TRP LEU LYS ASP ASN SEQRES 24 A 434 SER GLN ASN PRO LYS ASN TYR ASP TYR THR GLN GLY TYR SEQRES 25 A 434 SER THR CYS HIS PHE TRP THR ASN PHE GLU ILE VAL ASP SEQRES 26 A 434 LEU ASP PHE LEU ARG SER GLU PRO TYR GLU LYS TYR MET SEQRES 27 A 434 GLN TYR LEU GLU GLU LYS GLY GLY PHE TYR TYR GLU ARG SEQRES 28 A 434 TRP GLY ASP ALA PRO VAL ARG SER LEU ALA LEU ALA LEU SEQRES 29 A 434 PHE ALA ASP LYS SER SER ILE HIS TRP PHE ARG ASP ILE SEQRES 30 A 434 GLY TYR HIS HIS THR PRO TYR THR ASN CYS PRO THR CYS SEQRES 31 A 434 PRO ALA ASP SER ASP ARG CYS ASN GLY ASN CYS VAL PRO SEQRES 32 A 434 GLY LYS PHE THR PRO TRP SER ASP LEU ASP ASN GLN ASN SEQRES 33 A 434 CYS GLN ALA THR TRP ILE ARG HIS SER MET SER GLU GLU SEQRES 34 A 434 GLU LEU GLU MET TYR SEQRES 1 B 434 SER MET ASN GLU ASN TYR LEU GLN ALA VAL LYS ASP SER SEQRES 2 B 434 ALA LYS SER GLN TYR ALA SER LEU ARG GLU SER TYR LYS SEQRES 3 B 434 SER ILE THR GLY LYS THR GLU SER ALA ASP GLU LEU PRO SEQRES 4 B 434 ASP HIS ASP ALA GLU VAL LEU ASP SER ILE MET ASP ARG SEQRES 5 B 434 LEU HIS GLU PRO LEU TYR GLU LYS ASP THR PHE ASP PRO SEQRES 6 B 434 ASN GLU VAL LEU ALA GLU ASN LYS GLN LEU TYR GLU GLU SEQRES 7 B 434 PHE LEU LEU GLN GLU ILE SER GLU PRO LYS VAL ASP ASN SEQRES 8 B 434 LEU VAL ARG SER GLY ASP PRO LEU ALA GLY LYS ALA LYS SEQRES 9 B 434 GLY THR ILE LEU SER LEU VAL ARG ASN SER ASP LEU GLU SEQRES 10 B 434 ASP ILE ILE SER SER ILE GLN GLN LEU GLU GLU GLU TYR SEQRES 11 B 434 ASN LYS ASN PHE GLY TYR PRO TYR THR PHE LEU ASN ASP SEQRES 12 B 434 GLU GLU PHE THR ASP GLU PHE LYS ASP GLY ILE LYS SER SEQRES 13 B 434 ILE LEU PRO LYS ASP ARG VAL VAL GLU PHE GLY THR ILE SEQRES 14 B 434 GLY PRO ASP ASN TRP ASN MET PRO ASP SER ILE ASP ARG SEQRES 15 B 434 GLU ARG TYR ASP GLN GLU MET ASP LYS MET SER LYS GLU SEQRES 16 B 434 ASN ILE GLN TYR ALA GLU VAL GLU SER TYR HIS ASN MET SEQRES 17 B 434 CYS ARG PHE TYR SER LYS GLU PHE TYR HIS HIS PRO LEU SEQRES 18 B 434 LEU SER LYS TYR LYS TYR VAL TRP ARG LEU GLU PRO ASN SEQRES 19 B 434 VAL ASN PHE TYR CYS LYS ILE ASN TYR ASP VAL PHE GLN SEQRES 20 B 434 PHE MET ASN LYS ASN ASP LYS ILE TYR GLY PHE VAL LEU SEQRES 21 B 434 ASN LEU TYR ASP SER PRO GLN THR ILE GLU THR LEU TRP SEQRES 22 B 434 THR SER THR MET ASP PHE VAL GLU GLU HIS PRO ASN TYR SEQRES 23 B 434 LEU ASN VAL ASN GLY ALA PHE ALA TRP LEU LYS ASP ASN SEQRES 24 B 434 SER GLN ASN PRO LYS ASN TYR ASP TYR THR GLN GLY TYR SEQRES 25 B 434 SER THR CYS HIS PHE TRP THR ASN PHE GLU ILE VAL ASP SEQRES 26 B 434 LEU ASP PHE LEU ARG SER GLU PRO TYR GLU LYS TYR MET SEQRES 27 B 434 GLN TYR LEU GLU GLU LYS GLY GLY PHE TYR TYR GLU ARG SEQRES 28 B 434 TRP GLY ASP ALA PRO VAL ARG SER LEU ALA LEU ALA LEU SEQRES 29 B 434 PHE ALA ASP LYS SER SER ILE HIS TRP PHE ARG ASP ILE SEQRES 30 B 434 GLY TYR HIS HIS THR PRO TYR THR ASN CYS PRO THR CYS SEQRES 31 B 434 PRO ALA ASP SER ASP ARG CYS ASN GLY ASN CYS VAL PRO SEQRES 32 B 434 GLY LYS PHE THR PRO TRP SER ASP LEU ASP ASN GLN ASN SEQRES 33 B 434 CYS GLN ALA THR TRP ILE ARG HIS SER MET SER GLU GLU SEQRES 34 B 434 GLU LEU GLU MET TYR HET GDP A 500 28 HET MN A 501 1 HET ACT A1465 4 HET GDP B 500 28 HET MN B 501 1 HET ACT B1465 4 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM ACT ACETATE ION FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 MN 2(MN 2+) FORMUL 5 ACT 2(C2 H3 O2 1-) FORMUL 9 HOH *578(H2 O) HELIX 1 1 ASP A 70 LEU A 83 1 14 HELIX 2 2 ASP A 94 LEU A 111 1 18 HELIX 3 3 ARG A 142 SER A 144 5 3 HELIX 4 4 ASP A 145 TYR A 160 1 16 HELIX 5 5 ASN A 161 PHE A 164 5 4 HELIX 6 6 THR A 177 LEU A 188 1 12 HELIX 7 7 GLY A 200 TRP A 204 5 5 HELIX 8 8 ASP A 211 GLU A 225 1 15 HELIX 9 9 VAL A 232 GLU A 245 1 14 HELIX 10 10 PHE A 246 SER A 253 5 8 HELIX 11 11 ASP A 274 ASN A 282 1 9 HELIX 12 12 SER A 295 ILE A 299 5 5 HELIX 13 13 THR A 301 HIS A 313 1 13 HELIX 14 14 PRO A 314 LEU A 317 5 4 HELIX 15 15 ALA A 322 ASP A 328 1 7 HELIX 16 16 ASN A 332 THR A 339 1 8 HELIX 17 17 LEU A 356 SER A 361 1 6 HELIX 18 18 SER A 361 GLY A 375 1 15 HELIX 19 19 GLY A 375 GLU A 380 1 6 HELIX 20 20 GLY A 383 ALA A 396 1 14 HELIX 21 21 ASP A 397 SER A 399 5 3 HELIX 22 22 TRP A 439 GLN A 445 5 7 HELIX 23 23 CYS A 447 MET A 456 1 10 HELIX 24 24 SER A 457 GLU A 462 1 6 HELIX 25 25 ASP B 72 HIS B 84 1 13 HELIX 26 26 ASP B 94 LEU B 111 1 18 HELIX 27 27 ARG B 142 SER B 144 5 3 HELIX 28 28 ASP B 145 TYR B 160 1 16 HELIX 29 29 ASN B 161 PHE B 164 5 4 HELIX 30 30 THR B 177 ILE B 187 1 11 HELIX 31 31 GLY B 200 TRP B 204 5 5 HELIX 32 32 ASP B 211 GLU B 225 1 15 HELIX 33 33 VAL B 232 GLU B 245 1 14 HELIX 34 34 PHE B 246 SER B 253 5 8 HELIX 35 35 ASP B 274 ASN B 282 1 9 HELIX 36 36 SER B 295 ILE B 299 5 5 HELIX 37 37 THR B 301 HIS B 313 1 13 HELIX 38 38 PRO B 314 LEU B 317 5 4 HELIX 39 39 ALA B 322 ASP B 328 1 7 HELIX 40 40 ASN B 332 THR B 339 1 8 HELIX 41 41 LEU B 356 ARG B 360 1 5 HELIX 42 42 SER B 361 GLY B 375 1 15 HELIX 43 43 GLY B 375 GLU B 380 1 6 HELIX 44 44 GLY B 383 ALA B 396 1 14 HELIX 45 45 ASP B 397 SER B 399 5 3 HELIX 46 46 TRP B 439 GLN B 445 5 7 HELIX 47 47 CYS B 447 MET B 456 1 10 HELIX 48 48 SER B 457 GLU B 462 1 6 SHEET 1 AA 7 VAL A 194 THR A 198 0 SHEET 2 AA 7 TYR A 168 ASN A 172 1 O TYR A 168 N GLU A 195 SHEET 3 AA 7 GLY A 135 LEU A 140 1 O ILE A 137 N THR A 169 SHEET 4 AA 7 TYR A 257 ARG A 260 1 O TYR A 257 N THR A 136 SHEET 5 AA 7 GLU A 352 ASP A 355 -1 O GLU A 352 N ARG A 260 SHEET 6 AA 7 TYR A 286 PHE A 288 -1 O GLY A 287 N ILE A 353 SHEET 7 AA 7 ILE A 401 TRP A 403 1 O HIS A 402 N PHE A 288 SHEET 1 AB 3 ASN A 266 PHE A 267 0 SHEET 2 AB 3 TYR A 409 HIS A 411 -1 O HIS A 410 N ASN A 266 SHEET 3 AB 3 TYR A 414 ASN A 416 -1 O TYR A 414 N HIS A 411 SHEET 1 AC 2 ASN A 291 TYR A 293 0 SHEET 2 AC 2 CYS A 345 PHE A 347 -1 O HIS A 346 N LEU A 292 SHEET 1 BA 7 VAL B 194 THR B 198 0 SHEET 2 BA 7 TYR B 168 ASN B 172 1 O TYR B 168 N GLU B 195 SHEET 3 BA 7 GLY B 135 LEU B 140 1 O ILE B 137 N THR B 169 SHEET 4 BA 7 TYR B 257 ARG B 260 1 O TYR B 257 N THR B 136 SHEET 5 BA 7 GLU B 352 ASP B 355 -1 O GLU B 352 N ARG B 260 SHEET 6 BA 7 TYR B 286 PHE B 288 -1 O GLY B 287 N ILE B 353 SHEET 7 BA 7 ILE B 401 TRP B 403 1 O HIS B 402 N PHE B 288 SHEET 1 BB 3 ASN B 266 PHE B 267 0 SHEET 2 BB 3 TYR B 409 HIS B 411 -1 O HIS B 410 N ASN B 266 SHEET 3 BB 3 TYR B 414 ASN B 416 -1 O TYR B 414 N HIS B 411 SHEET 1 BC 2 ASN B 291 LEU B 292 0 SHEET 2 BC 2 HIS B 346 PHE B 347 -1 O HIS B 346 N LEU B 292 SSBOND 1 CYS A 269 CYS A 427 1555 1555 2.16 SSBOND 2 CYS A 345 CYS A 447 1555 1555 2.05 SSBOND 3 CYS A 417 CYS A 431 1555 1555 2.09 SSBOND 4 CYS B 269 CYS B 427 1555 1555 2.17 SSBOND 5 CYS B 345 CYS B 447 1555 1555 2.04 SSBOND 6 CYS B 417 CYS B 431 1555 1555 2.09 LINK OE1 GLU A 262 MN MN A 501 1555 1555 2.17 LINK NE2 HIS A 411 MN MN A 501 1555 1555 2.41 LINK O2A GDP A 500 MN MN A 501 1555 1555 2.24 LINK O1B GDP A 500 MN MN A 501 1555 1555 2.16 LINK MN MN A 501 O HOH A2177 1555 1555 2.32 LINK MN MN A 501 O HOH A2258 1555 1555 2.32 LINK OE1 GLU B 262 MN MN B 501 1555 1555 2.18 LINK NE2 HIS B 411 MN MN B 501 1555 1555 2.42 LINK O3B GDP B 500 MN MN B 501 1555 1555 2.18 LINK O2A GDP B 500 MN MN B 501 1555 1555 2.27 LINK MN MN B 501 O HOH B2171 1555 1555 2.39 LINK MN MN B 501 O HOH B2243 1555 1555 2.37 CISPEP 1 THR A 412 PRO A 413 0 3.51 CISPEP 2 THR B 412 PRO B 413 0 1.26 SITE 1 AC1 22 LEU A 140 VAL A 141 ARG A 142 ASP A 145 SITE 2 AC1 22 ASN A 172 ASP A 173 TRP A 204 TYR A 229 SITE 3 AC1 22 SER A 234 TYR A 235 MET A 238 GLU A 262 SITE 4 AC1 22 PRO A 263 HIS A 411 MN A 501 HOH A2070 SITE 5 AC1 22 HOH A2071 HOH A2105 HOH A2158 HOH A2232 SITE 6 AC1 22 HOH A2258 HOH A2300 SITE 1 AC2 5 GLU A 262 HIS A 411 GDP A 500 HOH A2177 SITE 2 AC2 5 HOH A2258 SITE 1 AC3 19 LEU B 140 VAL B 141 ARG B 142 ASP B 145 SITE 2 AC3 19 ASN B 172 ASP B 173 TYR B 229 SER B 234 SITE 3 AC3 19 TYR B 235 MET B 238 GLU B 262 PRO B 263 SITE 4 AC3 19 HIS B 411 MN B 501 HOH B2074 HOH B2075 SITE 5 AC3 19 HOH B2105 HOH B2153 HOH B2219 SITE 1 AC4 5 GLU B 262 HIS B 411 GDP B 500 HOH B2171 SITE 2 AC4 5 HOH B2243 SITE 1 AC5 6 LEU A 83 HIS A 84 PRO A 86 LYS A 327 SITE 2 AC5 6 TYR A 336 HOH A2007 SITE 1 AC6 5 HIS B 84 PRO B 86 LYS B 327 TYR B 336 SITE 2 AC6 5 HOH B2005 CRYST1 61.215 102.621 162.651 90.00 90.00 90.00 P 21 21 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 0.016336 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009745 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006148 0.00000 MTRIX1 1 0.745700 0.662800 0.068830 -11.77000 1 MTRIX2 1 0.662600 -0.748400 0.027930 34.73000 1 MTRIX3 1 0.070020 0.024780 -0.997200 -35.09000 1