HEADER TRANSFERASE 19-AUG-15 2N6D TITLE NMR STRUCTURE OF THE 140-315 FRAGMENT OF THE N-ACETYLGLUCOSAMINE-1- TITLE 2 PHOSPHATE TRANSFERASE, ALPHA AND BETA SUBUNITS COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLGLUCOSAMINE-1-PHOSPHOTRANSFERASE SUBUNITS COMPND 3 ALPHA/BETA; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 135-305; COMPND 6 SYNONYM: GLCNAC-1-PHOSPHOTRANSFERASE SUBUNITS ALPHA/BETA, STEALTH COMPND 7 PROTEIN GNPTAB, UDP-N-ACETYLGLUCOSAMINE-1-PHOSPHOTRANSFERASE SUBUNITS COMPND 8 ALPHA/BETA, N-ACETYLGLUCOSAMINE-1-PHOSPHOTRANSFERASE SUBUNIT ALPHA, COMPND 9 N-ACETYLGLUCOSAMINE-1-PHOSPHOTRANSFERASE SUBUNIT BETA; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GNPTAB, GNPTA, KIAA1208; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS PSI-BIOLOGY, N-ACETYLGLUCOSAMINE-1-PHOSPHATE TRANSFERASE, KEYWDS 2 TRANSFERASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL KEYWDS 3 GENOMICS, JCSG EXPDTA SOLUTION NMR NUMMDL 19 AUTHOR P.SERRANO,M.GERALT,K.WUTHRICH,JOINT CENTER FOR STRUCTURAL GENOMICS AUTHOR 2 (JCSG) REVDAT 2 14-JUN-23 2N6D 1 REMARK SEQADV REVDAT 1 14-OCT-15 2N6D 0 JRNL AUTH P.SERRANO,K.WUTHRICH,M.GERALT JRNL TITL NMR STRUCTURE OF THE 140-315 FRAGMENT OF THE JRNL TITL 2 N-ACETYLGLUCOSAMINE-1-PHOSPHATE TRANSFERASE, ALPHA AND BETA JRNL TITL 3 SUBUNITS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT, P. ET AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SEMI-AUTOMATED STRUCTURE DETERMINATION REMARK 3 WITH THE J-UNIO SUITE REMARK 4 REMARK 4 2N6D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000104478. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.24 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM [U-98% 13C; U-98% 15N] REMARK 210 PROTEIN, 50 MM SODIUM CHLORIDE, REMARK 210 20 MM SODIUM PHOSPHATE, 5 MM REMARK 210 SODIUM AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 3D 1H-15N NOESY; APSY REMARK 210 4D-HACANH; APSY 5D-CBCACONH; REMARK 210 APSY 5D-HACACONH REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 19 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 4 TYR A 128 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 5 LEU A 114 CB - CG - CD1 ANGL. DEV. = 10.3 DEGREES REMARK 500 5 TYR A 128 CB - CG - CD1 ANGL. DEV. = -4.8 DEGREES REMARK 500 7 TYR A 78 CB - CG - CD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 7 TYR A 128 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 7 TYR A 168 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 9 LEU A 114 CB - CA - C ANGL. DEV. = 12.0 DEGREES REMARK 500 11 ARG A 71 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 11 TYR A 128 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES REMARK 500 13 TYR A 78 CB - CG - CD1 ANGL. DEV. = -4.2 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 1 LYS A 67 33.12 -140.57 REMARK 500 1 LYS A 83 35.57 -78.56 REMARK 500 1 MET A 91 -179.14 -69.49 REMARK 500 1 ASP A 93 23.74 -170.65 REMARK 500 1 THR A 103 20.17 -68.11 REMARK 500 1 SER A 119 67.52 -159.00 REMARK 500 1 SER A 120 -74.50 -130.84 REMARK 500 1 LEU A 125 21.49 -159.44 REMARK 500 1 GLN A 126 92.19 -167.01 REMARK 500 1 GLU A 130 -46.00 -155.17 REMARK 500 1 THR A 151 12.57 -150.84 REMARK 500 1 ASN A 154 -31.04 -157.18 REMARK 500 2 PRO A 10 -164.75 -76.39 REMARK 500 2 ALA A 11 84.86 -160.37 REMARK 500 2 LYS A 41 19.85 -144.69 REMARK 500 2 VAL A 58 -61.62 -107.41 REMARK 500 2 LEU A 66 37.81 -80.35 REMARK 500 2 TRP A 75 -167.33 -118.01 REMARK 500 2 GLU A 84 56.00 -93.75 REMARK 500 2 ASP A 93 7.50 -158.53 REMARK 500 2 PRO A 115 8.49 -62.40 REMARK 500 2 GLU A 116 -49.51 76.41 REMARK 500 2 LEU A 125 38.10 -154.67 REMARK 500 2 GLN A 126 114.82 -160.61 REMARK 500 2 SER A 129 46.00 -71.46 REMARK 500 2 GLU A 130 -54.12 -171.07 REMARK 500 2 LYS A 152 12.35 -62.09 REMARK 500 2 ASN A 154 -27.96 -170.14 REMARK 500 3 PRO A 10 -169.09 -73.56 REMARK 500 3 ASN A 15 69.16 -106.60 REMARK 500 3 LYS A 83 26.72 -75.38 REMARK 500 3 THR A 103 32.36 -78.27 REMARK 500 3 LYS A 105 39.15 -84.59 REMARK 500 3 GLN A 109 -71.29 -74.43 REMARK 500 3 LYS A 113 32.88 -98.67 REMARK 500 3 GLU A 116 -66.98 174.55 REMARK 500 3 ASN A 117 -9.76 -58.24 REMARK 500 3 SER A 120 -77.14 -65.67 REMARK 500 3 LEU A 125 18.62 -153.37 REMARK 500 3 GLN A 126 80.90 -155.03 REMARK 500 3 ASP A 143 18.57 47.38 REMARK 500 4 ALA A 11 75.34 -153.61 REMARK 500 4 ALA A 14 24.62 -73.69 REMARK 500 4 ASN A 42 85.91 -153.74 REMARK 500 4 LYS A 67 -165.07 -161.28 REMARK 500 4 ASN A 69 78.65 -156.83 REMARK 500 4 TRP A 75 -169.18 -121.63 REMARK 500 4 LYS A 83 45.78 -73.06 REMARK 500 4 THR A 103 48.75 -103.44 REMARK 500 4 LYS A 105 -82.99 -137.14 REMARK 500 REMARK 500 THIS ENTRY HAS 304 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 10 ALA A 11 1 137.98 REMARK 500 PRO A 10 ALA A 11 3 149.85 REMARK 500 LEU A 162 THR A 163 3 142.51 REMARK 500 PRO A 10 ALA A 11 4 148.98 REMARK 500 TRP A 75 ARG A 76 6 148.61 REMARK 500 ARG A 76 GLY A 77 6 145.45 REMARK 500 TYR A 128 SER A 129 6 138.03 REMARK 500 PRO A 10 ALA A 11 7 130.37 REMARK 500 TRP A 171 ASP A 172 7 -144.53 REMARK 500 PRO A 10 ALA A 11 8 147.95 REMARK 500 TYR A 128 SER A 129 8 141.52 REMARK 500 PRO A 10 ALA A 11 9 143.45 REMARK 500 PRO A 10 ALA A 11 11 147.83 REMARK 500 GLY A 87 LEU A 88 11 -145.27 REMARK 500 PRO A 10 ALA A 11 12 140.69 REMARK 500 LYS A 121 VAL A 122 12 -148.16 REMARK 500 PRO A 10 ALA A 11 14 143.23 REMARK 500 LEU A 147 ASN A 148 16 -142.56 REMARK 500 LYS A 41 ASN A 42 17 147.64 REMARK 500 ASP A 93 LEU A 94 17 142.83 REMARK 500 SER A 165 PRO A 166 17 148.41 REMARK 500 PRO A 10 ALA A 11 18 138.28 REMARK 500 PRO A 10 ALA A 11 19 143.57 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 4 TYR A 128 0.08 SIDE CHAIN REMARK 500 6 TYR A 128 0.10 SIDE CHAIN REMARK 500 6 TYR A 168 0.07 SIDE CHAIN REMARK 500 9 TYR A 25 0.08 SIDE CHAIN REMARK 500 9 ARG A 76 0.10 SIDE CHAIN REMARK 500 11 ARG A 71 0.08 SIDE CHAIN REMARK 500 12 TYR A 128 0.12 SIDE CHAIN REMARK 500 15 ARG A 76 0.08 SIDE CHAIN REMARK 500 17 TYR A 128 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 25760 RELATED DB: BMRB REMARK 900 RELATED ID: JCSG-424817 RELATED DB: TARGETTRACK DBREF 2N6D A 2 172 UNP Q3T906 GNPTA_HUMAN 135 305 SEQADV 2N6D MET A 1 UNP Q3T906 INITIATING METHIONINE SEQRES 1 A 172 MET LYS VAL PRO MET LEU VAL LEU ASP PRO ALA LEU PRO SEQRES 2 A 172 ALA ASN ILE THR LEU LYS ASP LEU PRO SER LEU TYR PRO SEQRES 3 A 172 SER PHE HIS SER ALA SER ASP ILE PHE ASN VAL ALA LYS SEQRES 4 A 172 PRO LYS ASN PRO SER THR ASN VAL SER VAL VAL VAL PHE SEQRES 5 A 172 ASP SER THR LYS ASP VAL GLU ASP ALA HIS SER GLY LEU SEQRES 6 A 172 LEU LYS GLY ASN SER ARG GLN THR VAL TRP ARG GLY TYR SEQRES 7 A 172 LEU THR THR ASP LYS GLU VAL PRO GLY LEU VAL LEU MET SEQRES 8 A 172 GLN ASP LEU ALA PHE LEU SER GLY PHE PRO PRO THR PHE SEQRES 9 A 172 LYS GLU THR ASN GLN LEU LYS THR LYS LEU PRO GLU ASN SEQRES 10 A 172 LEU SER SER LYS VAL LYS LEU LEU GLN LEU TYR SER GLU SEQRES 11 A 172 ALA SER VAL ALA LEU LEU LYS LEU ASN ASN PRO LYS ASP SEQRES 12 A 172 PHE GLN GLU LEU ASN LYS GLN THR LYS LYS ASN MET THR SEQRES 13 A 172 ILE ASP GLY LYS GLU LEU THR ILE SER PRO ALA TYR LEU SEQRES 14 A 172 LEU TRP ASP HELIX 1 1 TYR A 25 HIS A 29 5 5 HELIX 2 2 SER A 54 GLY A 64 1 11 HELIX 3 3 GLU A 106 THR A 112 1 7 HELIX 4 4 PRO A 115 SER A 119 5 5 HELIX 5 5 ASN A 140 ASN A 148 1 9 SHEET 1 A 2 MET A 5 LEU A 8 0 SHEET 2 A 2 VAL A 74 GLY A 77 -1 O TRP A 75 N VAL A 7 SHEET 1 B 2 ASP A 33 LYS A 39 0 SHEET 2 B 2 ASN A 42 VAL A 51 -1 O VAL A 47 N VAL A 37 SHEET 1 C 2 VAL A 89 LEU A 90 0 SHEET 2 C 2 TYR A 168 LEU A 169 -1 O LEU A 169 N VAL A 89 SHEET 1 D 3 LEU A 94 LEU A 97 0 SHEET 2 D 3 ALA A 134 LEU A 138 -1 O LEU A 136 N ALA A 95 SHEET 3 D 3 VAL A 122 LYS A 123 -1 N LYS A 123 O LYS A 137 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1