HEADER TRANSFERASE 28-APR-20 6YV8 TITLE MANNOSYLTRANSFERASE PCMANGT FROM PYROBACULUM CALIDIFONTIS IN COMPLEX TITLE 2 WITH GDP AND MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSYL TRANSFERASE, FAMILY 2; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GLYCOSYL TRANSFERASE, FAMILY 2; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROBACULUM CALIDIFONTIS (STRAIN JCM 11548 / SOURCE 3 VA1); SOURCE 4 ORGANISM_TAXID: 410359; SOURCE 5 STRAIN: JCM 11548 / VA1; SOURCE 6 GENE: PCAL_0472; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: PYROBACULUM CALIDIFONTIS (STRAIN JCM 11548 / SOURCE 12 VA1); SOURCE 13 ORGANISM_TAXID: 410359; SOURCE 14 STRAIN: JCM 11548 / VA1; SOURCE 15 GENE: PCAL_0472; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PLASMID KEYWDS GLYCOSYLTRANSFERASE MEMBRANE PROTEIN MANNOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.DIVNE,R.GANDINI REVDAT 2 05-AUG-20 6YV8 1 JRNL LINK REVDAT 1 22-JUL-20 6YV8 0 JRNL AUTH R.GANDINI,T.REICHENBACH,O.SPADIUT,T.C.TAN,D.C.KALYANI, JRNL AUTH 2 C.DIVNE JRNL TITL A TRANSMEMBRANE CRENARCHAEAL MANNOSYLTRANSFERASE IS INVOLVED JRNL TITL 2 IN N-GLYCAN BIOSYNTHESIS AND DISPLAYS AN UNEXPECTED MINIMAL JRNL TITL 3 CELLULOSE-SYNTHASE-LIKE FOLD. JRNL REF J.MOL.BIOL. V. 432 4658 2020 JRNL REFN ESSN 1089-8638 JRNL PMID 32569746 JRNL DOI 10.1016/J.JMB.2020.06.016 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.14_3260: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 28575 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.236 REMARK 3 R VALUE (WORKING SET) : 0.233 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 2.6650 - 2.6000 0.97 1800 136 0.3939 0.4469 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.012 5602 REMARK 3 ANGLE : 1.498 7686 REMARK 3 CHIRALITY : 0.081 867 REMARK 3 PLANARITY : 0.012 967 REMARK 3 DIHEDRAL : 20.796 2008 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6YV8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108357. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28580 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 48.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 12.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 9.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 MM HEPES (PH 7.5), 20% PEG 4000, REMARK 280 10% ISOPROPANOL, 10 MM MNCL2 AND 2% 1,2,3-HEPTANETRIOL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 25.49900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 82.20900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.82200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 82.20900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 25.49900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.82200 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC 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 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 ALA A 168 REMARK 465 GLY A 169 REMARK 465 PRO A 170 REMARK 465 ALA A 171 REMARK 465 GLY A 172 REMARK 465 VAL A 173 REMARK 465 GLU A 174 REMARK 465 ASP A 175 REMARK 465 SER A 176 REMARK 465 TYR A 177 REMARK 465 ALA B 168 REMARK 465 GLY B 169 REMARK 465 PRO B 170 REMARK 465 ALA B 171 REMARK 465 GLY B 172 REMARK 465 VAL B 173 REMARK 465 GLU B 174 REMARK 465 ASP B 175 REMARK 465 SER B 176 REMARK 465 TYR B 177 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 NZ LYS A 271 NH2 ARG A 274 2.12 REMARK 500 OE1 GLU A 54 O2' GDP A 401 2.14 REMARK 500 OD1 ASN A 53 OG SER A 84 2.17 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 GLU A 97 CA - CB - CG ANGL. DEV. = -17.0 DEGREES REMARK 500 LEU A 212 CA - CB - CG ANGL. DEV. = -15.6 DEGREES REMARK 500 CYS A 245 CA - CB - SG ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 252 NH1 - CZ - NH2 ANGL. DEV. = -9.9 DEGREES REMARK 500 ARG A 252 NE - CZ - NH2 ANGL. DEV. = 6.9 DEGREES REMARK 500 SER A 315 CB - CA - C ANGL. DEV. = 14.0 DEGREES REMARK 500 SER A 315 N - CA - CB ANGL. DEV. = -12.8 DEGREES REMARK 500 LYS B 31 CD - CE - NZ ANGL. DEV. = 18.0 DEGREES REMARK 500 ARG B 143 CD - NE - CZ ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG B 143 NE - CZ - NH1 ANGL. DEV. = -19.1 DEGREES REMARK 500 ARG B 143 NE - CZ - NH2 ANGL. DEV. = 11.4 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 ALA A 83 73.41 61.20 REMARK 500 THR A 110 -38.35 -36.54 REMARK 500 GLU A 111 135.08 -175.19 REMARK 500 TRP A 192 -71.41 -161.63 REMARK 500 LEU A 201 108.63 -162.08 REMARK 500 LYS A 251 -63.87 79.56 REMARK 500 LYS A 277 64.13 73.91 REMARK 500 SER B 82 78.75 -102.26 REMARK 500 TRP B 192 -74.80 -163.03 REMARK 500 LEU B 201 111.11 -160.47 REMARK 500 LYS B 251 -64.85 76.53 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 THR A 110 GLU A 111 -143.97 REMARK 500 LEU A 316 PRO A 317 130.10 REMARK 500 LYS B 31 PRO B 32 -124.65 REMARK 500 LEU B 330 TYR B 331 148.53 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 GLU A 111 0.07 SIDE CHAIN REMARK 500 ARG B 143 0.14 SIDE CHAIN 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 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 137 OD2 REMARK 620 2 GDP A 401 O1B 140.3 REMARK 620 3 GDP A 401 O1A 124.9 78.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 137 OD2 REMARK 620 2 GDP B 401 O2B 156.0 REMARK 620 3 GDP B 401 O2A 113.7 89.0 REMARK 620 N 1 2 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 402 DBREF 6YV8 A 1 356 UNP A3MTD6 A3MTD6_PYRCJ 1 356 DBREF 6YV8 B 2 356 UNP A3MTD6 A3MTD6_PYRCJ 2 356 SEQRES 1 A 356 MET LEU LEU GLU ALA ILE ALA ILE ALA LEU THR ALA ALA SEQRES 2 A 356 HIS PHE GLY ALA PRO LEU LEU TYR TYR TRP ARG ALA LYS SEQRES 3 A 356 ARG TRP LEU LYS LYS PRO TRP ASP VAL ALA PRO ASP PRO SEQRES 4 A 356 THR TYR ARG PRO ARG VAL THR VAL ILE VAL PRO THR TYR SEQRES 5 A 356 ASN GLU ALA PRO LEU ILE GLU GLU LYS LEU ASP ASN ILE SEQRES 6 A 356 TYR GLU GLN ASP TYR PRO ARG ASP LYS LEU GLU VAL VAL SEQRES 7 A 356 VAL VAL ASP SER ALA SER THR ASP GLY THR PRO SER ALA SEQRES 8 A 356 VAL ARG ARG TRP ALA GLU THR HIS PRO ASP LEU ALA LEU SEQRES 9 A 356 THR LEU VAL GLU GLU THR GLU ARG ARG GLY LYS ALA HIS SEQRES 10 A 356 ALA LEU ASN THR ALA LEU ARG HIS ALA THR GLY GLU ILE SEQRES 11 A 356 VAL VAL ILE THR ASP ALA ASP ALA LEU TRP PRO ALA ARG SEQRES 12 A 356 ASP THR LEU ALA ASN ALA VAL LYS TRP LEU ALA ASP PRO SEQRES 13 A 356 THR VAL GLY ALA VAL SER CYS VAL LYS ARG PRO ALA GLY SEQRES 14 A 356 PRO ALA GLY VAL GLU ASP SER TYR ARG ASP PHE TYR ASN SEQRES 15 A 356 VAL LEU ARG VAL ALA GLU SER LYS ALA TRP ALA THR PRO SEQRES 16 A 356 ILE PHE HIS GLY GLU LEU ALA ALA PHE LYS ARG GLU LEU SEQRES 17 A 356 LEU GLU ARG LEU GLY GLY PHE PRO THR ASP VAL GLY ALA SEQRES 18 A 356 ASP ASP SER HIS THR ALA THR LYS ILE ALA MET MET GLY SEQRES 19 A 356 TYR ARG ALA ILE THR PRO PRO ASP VAL VAL CYS VAL GLU SEQRES 20 A 356 ALA VAL PRO LYS ARG GLY TYR HIS ALA TRP ARG ILE ARG SEQRES 21 A 356 ARG ALA GLN HIS LEU VAL GLN HIS PHE ALA LYS ALA ILE SEQRES 22 A 356 ARG ASP GLY LYS ALA PRO PRO PRO PHE LYS PRO ILE LEU SEQRES 23 A 356 HIS ALA GLU ALA TYR LEU HIS LEU ALA ASN PRO TRP ALA SEQRES 24 A 356 LEU PRO THR ALA ALA ALA ALA LEU ALA ALA ALA ALA ALA SEQRES 25 A 356 ALA GLY SER LEU PRO ALA ALA ALA LEU LEU ALA THR GLY SEQRES 26 A 356 ALA ALA LEU ALA LEU TYR LYS PRO TYR ARG THR TRP THR SEQRES 27 A 356 THR MET GLN ALA TYR LEU ILE ALA ALA ALA VAL LYS ASN SEQRES 28 A 356 LEU TRP ASP LYS GLU SEQRES 1 B 355 LEU LEU GLU ALA ILE ALA ILE ALA LEU THR ALA ALA HIS SEQRES 2 B 355 PHE GLY ALA PRO LEU LEU TYR TYR TRP ARG ALA LYS ARG SEQRES 3 B 355 TRP LEU LYS LYS PRO TRP ASP VAL ALA PRO ASP PRO THR SEQRES 4 B 355 TYR ARG PRO ARG VAL THR VAL ILE VAL PRO THR TYR ASN SEQRES 5 B 355 GLU ALA PRO LEU ILE GLU GLU LYS LEU ASP ASN ILE TYR SEQRES 6 B 355 GLU GLN ASP TYR PRO ARG ASP LYS LEU GLU VAL VAL VAL SEQRES 7 B 355 VAL ASP SER ALA SER THR ASP GLY THR PRO SER ALA VAL SEQRES 8 B 355 ARG ARG TRP ALA GLU THR HIS PRO ASP LEU ALA LEU THR SEQRES 9 B 355 LEU VAL GLU GLU THR GLU ARG ARG GLY LYS ALA HIS ALA SEQRES 10 B 355 LEU ASN THR ALA LEU ARG HIS ALA THR GLY GLU ILE VAL SEQRES 11 B 355 VAL ILE THR ASP ALA ASP ALA LEU TRP PRO ALA ARG ASP SEQRES 12 B 355 THR LEU ALA ASN ALA VAL LYS TRP LEU ALA ASP PRO THR SEQRES 13 B 355 VAL GLY ALA VAL SER CYS VAL LYS ARG PRO ALA GLY PRO SEQRES 14 B 355 ALA GLY VAL GLU ASP SER TYR ARG ASP PHE TYR ASN VAL SEQRES 15 B 355 LEU ARG VAL ALA GLU SER LYS ALA TRP ALA THR PRO ILE SEQRES 16 B 355 PHE HIS GLY GLU LEU ALA ALA PHE LYS ARG GLU LEU LEU SEQRES 17 B 355 GLU ARG LEU GLY GLY PHE PRO THR ASP VAL GLY ALA ASP SEQRES 18 B 355 ASP SER HIS THR ALA THR LYS ILE ALA MET MET GLY TYR SEQRES 19 B 355 ARG ALA ILE THR PRO PRO ASP VAL VAL CYS VAL GLU ALA SEQRES 20 B 355 VAL PRO LYS ARG GLY TYR HIS ALA TRP ARG ILE ARG ARG SEQRES 21 B 355 ALA GLN HIS LEU VAL GLN HIS PHE ALA LYS ALA ILE ARG SEQRES 22 B 355 ASP GLY LYS ALA PRO PRO PRO PHE LYS PRO ILE LEU HIS SEQRES 23 B 355 ALA GLU ALA TYR LEU HIS LEU ALA ASN PRO TRP ALA LEU SEQRES 24 B 355 PRO THR ALA ALA ALA ALA LEU ALA ALA ALA ALA ALA ALA SEQRES 25 B 355 GLY SER LEU PRO ALA ALA ALA LEU LEU ALA THR GLY ALA SEQRES 26 B 355 ALA LEU ALA LEU TYR LYS PRO TYR ARG THR TRP THR THR SEQRES 27 B 355 MET GLN ALA TYR LEU ILE ALA ALA ALA VAL LYS ASN LEU SEQRES 28 B 355 TRP ASP LYS GLU HET GDP A 401 28 HET MN A 402 1 HET GDP B 401 28 HET MN B 402 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MN MANGANESE (II) ION FORMUL 3 GDP 2(C10 H15 N5 O11 P2) FORMUL 4 MN 2(MN 2+) HELIX 1 AA1 MET A 1 LYS A 30 1 30 HELIX 2 AA2 GLU A 54 GLU A 67 1 14 HELIX 3 AA3 PRO A 71 ASP A 73 5 3 HELIX 4 AA4 GLY A 87 HIS A 99 1 13 HELIX 5 AA5 GLY A 114 HIS A 125 1 12 HELIX 6 AA6 ASP A 144 LEU A 153 1 10 HELIX 7 AA7 ASP A 179 TRP A 192 1 14 HELIX 8 AA8 ARG A 206 GLY A 213 1 8 HELIX 9 AA9 ALA A 221 MET A 233 1 13 HELIX 10 AB1 GLY A 253 ARG A 274 1 22 HELIX 11 AB2 PHE A 282 ALA A 295 1 14 HELIX 12 AB3 ALA A 295 ALA A 313 1 19 HELIX 13 AB4 PRO A 317 ALA A 329 1 13 HELIX 14 AB5 TYR A 331 LYS A 355 1 25 HELIX 15 AB6 LEU B 3 LYS B 31 1 29 HELIX 16 AB7 GLU B 54 GLU B 67 1 14 HELIX 17 AB8 PRO B 71 ASP B 73 5 3 HELIX 18 AB9 GLY B 87 HIS B 99 1 13 HELIX 19 AC1 GLY B 114 ARG B 124 1 11 HELIX 20 AC2 ASP B 144 LEU B 153 1 10 HELIX 21 AC3 ASP B 179 TRP B 192 1 14 HELIX 22 AC4 ARG B 206 GLY B 213 1 8 HELIX 23 AC5 ALA B 221 MET B 233 1 13 HELIX 24 AC6 GLY B 253 ARG B 274 1 22 HELIX 25 AC7 PHE B 282 ALA B 295 1 14 HELIX 26 AC8 ALA B 295 ALA B 313 1 19 HELIX 27 AC9 LEU B 316 LEU B 328 1 13 HELIX 28 AD1 TYR B 331 GLU B 356 1 26 SHEET 1 AA1 7 ALA A 103 GLU A 108 0 SHEET 2 AA1 7 LEU A 75 ASP A 81 1 N VAL A 77 O THR A 105 SHEET 3 AA1 7 VAL A 45 THR A 51 1 N VAL A 47 O GLU A 76 SHEET 4 AA1 7 ILE A 130 ILE A 133 1 O VAL A 132 N ILE A 48 SHEET 5 AA1 7 ALA A 202 LYS A 205 -1 O PHE A 204 N VAL A 131 SHEET 6 AA1 7 VAL A 158 SER A 162 -1 N VAL A 161 O ALA A 203 SHEET 7 AA1 7 ARG A 236 ILE A 238 1 O ILE A 238 N SER A 162 SHEET 1 AA2 2 VAL A 164 ARG A 166 0 SHEET 2 AA2 2 VAL A 244 VAL A 246 1 O CYS A 245 N ARG A 166 SHEET 1 AA3 7 ALA B 103 GLU B 109 0 SHEET 2 AA3 7 LEU B 75 SER B 82 1 N ASP B 81 O VAL B 107 SHEET 3 AA3 7 VAL B 45 THR B 51 1 N THR B 51 O VAL B 80 SHEET 4 AA3 7 ILE B 130 ILE B 133 1 O VAL B 132 N THR B 46 SHEET 5 AA3 7 ALA B 202 LYS B 205 -1 O ALA B 202 N ILE B 133 SHEET 6 AA3 7 VAL B 158 SER B 162 -1 N VAL B 161 O ALA B 203 SHEET 7 AA3 7 ARG B 236 ILE B 238 1 O ILE B 238 N SER B 162 SHEET 1 AA4 2 VAL B 164 ARG B 166 0 SHEET 2 AA4 2 VAL B 244 VAL B 246 1 O CYS B 245 N VAL B 164 SSBOND 1 CYS A 163 CYS A 245 1555 1555 2.17 SSBOND 2 CYS B 163 CYS B 245 1555 1555 2.08 LINK OD2 ASP A 137 MN MN A 402 1555 1555 2.70 LINK O1B GDP A 401 MN MN A 402 1555 1555 2.06 LINK O1A GDP A 401 MN MN A 402 1555 1555 2.18 LINK OD2 ASP B 137 MN MN B 402 1555 1555 2.47 LINK O2B GDP B 401 MN MN B 402 1555 1555 2.18 LINK O2A GDP B 401 MN MN B 402 1555 1555 1.97 CISPEP 1 LEU A 212 GLY A 213 0 -14.61 CISPEP 2 LEU B 212 GLY B 213 0 -14.96 SITE 1 AC1 15 PRO A 50 THR A 51 TYR A 52 GLU A 54 SITE 2 AC1 15 VAL A 80 SER A 82 ARG A 112 GLY A 114 SITE 3 AC1 15 ALA A 118 ASP A 135 ALA A 136 TRP A 257 SITE 4 AC1 15 ARG A 260 ARG A 261 MN A 402 SITE 1 AC2 2 ASP A 137 GDP A 401 SITE 1 AC3 16 PRO B 50 THR B 51 TYR B 52 GLU B 54 SITE 2 AC3 16 VAL B 80 SER B 82 ARG B 112 GLY B 114 SITE 3 AC3 16 LYS B 115 ALA B 118 ASP B 135 ALA B 136 SITE 4 AC3 16 TRP B 257 ARG B 260 ARG B 261 MN B 402 SITE 1 AC4 2 ASP B 137 GDP B 401 CRYST1 50.998 107.644 164.418 90.00 90.00 90.00 P 21 21 21 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 0.019609 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009290 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006082 0.00000