HEADER HYDROLASE 14-MAR-21 7NUT TITLE CRYSTAL STRUCTURE OF HUMAN AMDHD2 IN COMPLEX WITH ZN AND GLCN6P COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GLCNAC 6-P DEACETYLASE,AMIDOHYDROLASE DOMAIN-CONTAINING COMPND 5 PROTEIN 2; COMPND 6 EC: 3.5.1.25; COMPND 7 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: AMDHD2, CGI-14; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS N-ACETYLGLUCOSAMINE-6-PHOSPHATE DEACETYLASE, NAGA, AMIDOHYDROLASE KEYWDS 2 DOMAIN-CONTAINING PROTEIN 2, AMDHD2, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.RUEGENBERG,V.KROEF,U.BAUMANN,M.S.DENZEL REVDAT 4 31-JAN-24 7NUT 1 JRNL REVDAT 3 16-MAR-22 7NUT 1 JRNL REVDAT 2 05-MAY-21 7NUT 1 JRNL REVDAT 1 28-APR-21 7NUT 0 JRNL AUTH V.KROEF,S.RUEGENBERG,M.HORN,K.ALLMEROTH,L.EBERT,S.BOZKUS, JRNL AUTH 2 S.MIETHE,U.ELLING,B.SCHERMER,U.BAUMANN,M.S.DENZEL JRNL TITL GFPT2/GFAT2 AND AMDHD2 ACT IN TANDEM TO CONTROL THE JRNL TITL 2 HEXOSAMINE PATHWAY. JRNL REF ELIFE V. 11 2022 JRNL REFN ESSN 2050-084X JRNL PMID 35229715 JRNL DOI 10.7554/ELIFE.69223 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH V.KROEF,S.RUEGENBERG,M.HORN,K.ALLMEROTH,L.EBERT,S.BOZKUS, REMARK 1 AUTH 2 S.MIETHE,B.SCHERMER,U.BAUMANN,M.S.DENZEL REMARK 1 TITL GFAT2 AND AMDHD2 ACT IN TANDEM TO CONTROL THE HEXOSAMINE REMARK 1 TITL 2 BIOSYNTHETIC PATHWAY REMARK 1 REF BIORXIV 2021 REMARK 1 REFN ISSN 2692-8205 REMARK 1 DOI 10.1101/2021.04.23.441115 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 70754 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1981 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 48.7070 - 4.5722 0.99 5199 150 0.1614 0.1894 REMARK 3 2 4.5722 - 3.6294 1.00 5036 145 0.1472 0.1761 REMARK 3 3 3.6294 - 3.1707 1.00 4951 143 0.1771 0.2096 REMARK 3 4 3.1707 - 2.8809 1.00 4926 142 0.1892 0.2443 REMARK 3 5 2.8809 - 2.6744 1.00 4940 143 0.1918 0.2129 REMARK 3 6 2.6744 - 2.5167 1.00 4885 140 0.1850 0.1975 REMARK 3 7 2.5167 - 2.3907 1.00 4913 142 0.1858 0.2051 REMARK 3 8 2.3907 - 2.2866 1.00 4890 141 0.1875 0.2022 REMARK 3 9 2.2866 - 2.1986 1.00 4872 139 0.2102 0.2315 REMARK 3 10 2.1986 - 2.1227 1.00 4876 140 0.2368 0.2706 REMARK 3 11 2.1227 - 2.0564 1.00 4857 140 0.2600 0.3302 REMARK 3 12 2.0564 - 1.9976 1.00 4883 140 0.2849 0.3017 REMARK 3 13 1.9976 - 1.9450 1.00 4828 140 0.3026 0.2780 REMARK 3 14 1.9450 - 1.8980 0.97 4717 136 0.3227 0.3217 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.080 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.85 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 6 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): -25.1704 35.7299 -33.7876 REMARK 3 T TENSOR REMARK 3 T11: 0.6363 T22: 0.5907 REMARK 3 T33: 0.4996 T12: 0.1888 REMARK 3 T13: 0.0081 T23: -0.0104 REMARK 3 L TENSOR REMARK 3 L11: 1.4103 L22: 3.1524 REMARK 3 L33: 2.1351 L12: -0.8997 REMARK 3 L13: 0.0554 L23: 0.9166 REMARK 3 S TENSOR REMARK 3 S11: 0.0801 S12: -0.0483 S13: 0.3233 REMARK 3 S21: -0.3281 S22: -0.1431 S23: 0.2757 REMARK 3 S31: -0.8613 S32: -0.5486 S33: 0.0772 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 57 THROUGH 406 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.5414 13.7570 -31.5481 REMARK 3 T TENSOR REMARK 3 T11: 0.3002 T22: 0.3253 REMARK 3 T33: 0.2899 T12: -0.0615 REMARK 3 T13: 0.0202 T23: -0.0220 REMARK 3 L TENSOR REMARK 3 L11: 0.8557 L22: 1.5025 REMARK 3 L33: 1.5695 L12: -0.3268 REMARK 3 L13: 0.0393 L23: -0.1018 REMARK 3 S TENSOR REMARK 3 S11: 0.0355 S12: -0.0190 S13: 0.1181 REMARK 3 S21: -0.0630 S22: -0.0049 S23: -0.1803 REMARK 3 S31: -0.2766 S32: 0.2035 S33: -0.0245 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 9 THROUGH 56 ) REMARK 3 ORIGIN FOR THE GROUP (A): -52.4357 -16.7273 -28.1261 REMARK 3 T TENSOR REMARK 3 T11: 0.3840 T22: 0.6206 REMARK 3 T33: 0.5616 T12: -0.0210 REMARK 3 T13: 0.0067 T23: 0.0857 REMARK 3 L TENSOR REMARK 3 L11: 3.2384 L22: 0.2791 REMARK 3 L33: 1.0521 L12: 0.3273 REMARK 3 L13: 1.0398 L23: 0.3649 REMARK 3 S TENSOR REMARK 3 S11: -0.0639 S12: -0.1085 S13: -0.0473 REMARK 3 S21: -0.0606 S22: 0.0620 S23: 0.2443 REMARK 3 S31: 0.0648 S32: -0.5023 S33: -0.0233 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 57 THROUGH 406 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.1525 -23.7209 -35.0674 REMARK 3 T TENSOR REMARK 3 T11: 0.3195 T22: 0.2515 REMARK 3 T33: 0.3009 T12: -0.0036 REMARK 3 T13: -0.0401 T23: -0.0142 REMARK 3 L TENSOR REMARK 3 L11: 1.8267 L22: 1.2648 REMARK 3 L33: 1.6407 L12: 0.4576 REMARK 3 L13: -0.7582 L23: -0.4508 REMARK 3 S TENSOR REMARK 3 S11: -0.0700 S12: 0.0234 S13: -0.2608 REMARK 3 S21: -0.1043 S22: 0.0663 S23: -0.0320 REMARK 3 S31: 0.3685 S32: 0.0258 S33: -0.0055 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 9 THROUGH 84 OR REMARK 3 (RESID 85 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 86 REMARK 3 THROUGH 304 OR (RESID 305 THROUGH 306 AND REMARK 3 (NAME N OR NAME CA OR NAME C OR NAME O OR REMARK 3 NAME CB )) OR RESID 307 THROUGH 313 OR REMARK 3 (RESID 314 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 315 REMARK 3 THROUGH 406)) REMARK 3 SELECTION : CHAIN B REMARK 3 ATOM PAIRS NUMBER : 3584 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7NUT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292109571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS MAR 15, 2019 REMARK 200 DATA SCALING SOFTWARE : XDS MAR 15, 2019 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70760 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.898 REMARK 200 RESOLUTION RANGE LOW (A) : 48.707 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4600 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) : 1.97 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) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.16_3549 REMARK 200 STARTING MODEL: 2VHL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS TRIS PROPANE PH 8.25, 0.25 M REMARK 280 SODIUM NITRATE, 20 % PEG3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K 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 31.63050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.31050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 80.72450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.31050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.63050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 80.72450 REMARK 290 SMTRY3 4 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: 3600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -99.0 KCAL/MOL 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 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 ARG A 2 REMARK 465 GLY A 3 REMARK 465 GLU A 4 REMARK 465 GLN A 5 REMARK 465 ALA A 407 REMARK 465 ARG A 408 REMARK 465 GLN A 409 REMARK 465 MET B 1 REMARK 465 ARG B 2 REMARK 465 GLY B 3 REMARK 465 GLU B 4 REMARK 465 GLN B 5 REMARK 465 GLY B 6 REMARK 465 ALA B 7 REMARK 465 ALA B 8 REMARK 465 ALA B 407 REMARK 465 ARG B 408 REMARK 465 GLN B 409 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 GLU B 85 CG CD OE1 OE2 REMARK 470 ARG B 305 CG CD NE CZ NH1 NH2 REMARK 470 HIS B 306 CG ND1 CD2 CE1 NE2 REMARK 470 GLU B 314 CG CD OE1 OE2 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 B 601 O HOH B 610 2.01 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 NH2 ARG A 149 OE1 GLU B 29 1655 2.01 REMARK 500 NH2 ARG A 49 OD2 ASP A 405 4454 2.03 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 THR A 112 116.48 -39.84 REMARK 500 ALA A 165 -70.63 -62.77 REMARK 500 ALA A 167 -113.05 43.87 REMARK 500 HIS A 232 78.23 25.74 REMARK 500 PHE A 234 -33.13 85.19 REMARK 500 ASP A 244 72.32 -165.06 REMARK 500 HIS A 285 72.99 -153.33 REMARK 500 SER A 358 -67.57 -148.76 REMARK 500 GLU B 48 -84.08 -129.23 REMARK 500 THR B 112 116.24 -39.93 REMARK 500 ALA B 165 -73.74 -60.16 REMARK 500 ASP B 166 44.06 -143.58 REMARK 500 ALA B 167 -112.56 46.98 REMARK 500 HIS B 232 81.10 24.83 REMARK 500 PHE B 234 -31.45 84.05 REMARK 500 ASP B 244 73.52 -164.28 REMARK 500 ALA B 268 61.33 -100.44 REMARK 500 HIS B 285 73.92 -152.98 REMARK 500 SER B 358 -70.09 -149.97 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 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 143 OE1 REMARK 620 2 HIS A 211 NE2 93.7 REMARK 620 3 HIS A 232 NE2 103.7 97.2 REMARK 620 4 HOH A 602 O 135.8 97.9 116.8 REMARK 620 5 HOH A 684 O 84.3 171.5 91.3 78.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 143 OE2 REMARK 620 2 HIS B 211 NE2 92.7 REMARK 620 3 HIS B 232 NE2 100.8 100.6 REMARK 620 4 HOH B 601 O 123.8 99.7 129.5 REMARK 620 5 HOH B 610 O 93.1 156.6 100.5 58.6 REMARK 620 N 1 2 3 4 DBREF 7NUT A 1 409 UNP Q9Y303 NAGA_HUMAN 1 409 DBREF 7NUT B 1 409 UNP Q9Y303 NAGA_HUMAN 1 409 SEQRES 1 A 409 MET ARG GLY GLU GLN GLY ALA ALA GLY ALA ARG VAL LEU SEQRES 2 A 409 GLN PHE THR ASN CYS ARG ILE LEU ARG GLY GLY LYS LEU SEQRES 3 A 409 LEU ARG GLU ASP LEU TRP VAL ARG GLY GLY ARG ILE LEU SEQRES 4 A 409 ASP PRO GLU LYS LEU PHE PHE GLU GLU ARG ARG VAL ALA SEQRES 5 A 409 ASP GLU ARG ARG ASP CYS GLY GLY ARG ILE LEU ALA PRO SEQRES 6 A 409 GLY PHE ILE ASP VAL GLN ILE ASN GLY GLY PHE GLY VAL SEQRES 7 A 409 ASP PHE SER GLN ALA THR GLU ASP VAL GLY SER GLY VAL SEQRES 8 A 409 ALA LEU VAL ALA ARG ARG ILE LEU SER HIS GLY VAL THR SEQRES 9 A 409 SER PHE CYS PRO THR LEU VAL THR SER PRO PRO GLU VAL SEQRES 10 A 409 TYR HIS LYS VAL VAL PRO GLN ILE PRO VAL LYS SER GLY SEQRES 11 A 409 GLY PRO HIS GLY ALA GLY VAL LEU GLY LEU HIS LEU GLU SEQRES 12 A 409 GLY PRO PHE ILE SER ARG GLU LYS ARG GLY ALA HIS PRO SEQRES 13 A 409 GLU ALA HIS LEU ARG SER PHE GLU ALA ASP ALA PHE GLN SEQRES 14 A 409 ASP LEU LEU ALA THR TYR GLY PRO LEU ASP ASN VAL ARG SEQRES 15 A 409 ILE VAL THR LEU ALA PRO GLU LEU GLY ARG SER HIS GLU SEQRES 16 A 409 VAL ILE ARG ALA LEU THR ALA ARG GLY ILE CYS VAL SER SEQRES 17 A 409 LEU GLY HIS SER VAL ALA ASP LEU ARG ALA ALA GLU ASP SEQRES 18 A 409 ALA VAL TRP SER GLY ALA THR PHE ILE THR HIS LEU PHE SEQRES 19 A 409 ASN ALA MET LEU PRO PHE HIS HIS ARG ASP PRO GLY ILE SEQRES 20 A 409 VAL GLY LEU LEU THR SER ASP ARG LEU PRO ALA GLY ARG SEQRES 21 A 409 CYS ILE PHE TYR GLY MET ILE ALA ASP GLY THR HIS THR SEQRES 22 A 409 ASN PRO ALA ALA LEU ARG ILE ALA HIS ARG ALA HIS PRO SEQRES 23 A 409 GLN GLY LEU VAL LEU VAL THR ASP ALA ILE PRO ALA LEU SEQRES 24 A 409 GLY LEU GLY ASN GLY ARG HIS THR LEU GLY GLN GLN GLU SEQRES 25 A 409 VAL GLU VAL ASP GLY LEU THR ALA TYR VAL ALA GLY THR SEQRES 26 A 409 LYS THR LEU SER GLY SER ILE ALA PRO MET ASP VAL CYS SEQRES 27 A 409 VAL ARG HIS PHE LEU GLN ALA THR GLY CYS SER MET GLU SEQRES 28 A 409 SER ALA LEU GLU ALA ALA SER LEU HIS PRO ALA GLN LEU SEQRES 29 A 409 LEU GLY LEU GLU LYS SER LYS GLY THR LEU ASP PHE GLY SEQRES 30 A 409 ALA ASP ALA ASP PHE VAL VAL LEU ASP ASP SER LEU HIS SEQRES 31 A 409 VAL GLN ALA THR TYR ILE SER GLY GLU LEU VAL TRP GLN SEQRES 32 A 409 ALA ASP ALA ALA ARG GLN SEQRES 1 B 409 MET ARG GLY GLU GLN GLY ALA ALA GLY ALA ARG VAL LEU SEQRES 2 B 409 GLN PHE THR ASN CYS ARG ILE LEU ARG GLY GLY LYS LEU SEQRES 3 B 409 LEU ARG GLU ASP LEU TRP VAL ARG GLY GLY ARG ILE LEU SEQRES 4 B 409 ASP PRO GLU LYS LEU PHE PHE GLU GLU ARG ARG VAL ALA SEQRES 5 B 409 ASP GLU ARG ARG ASP CYS GLY GLY ARG ILE LEU ALA PRO SEQRES 6 B 409 GLY PHE ILE ASP VAL GLN ILE ASN GLY GLY PHE GLY VAL SEQRES 7 B 409 ASP PHE SER GLN ALA THR GLU ASP VAL GLY SER GLY VAL SEQRES 8 B 409 ALA LEU VAL ALA ARG ARG ILE LEU SER HIS GLY VAL THR SEQRES 9 B 409 SER PHE CYS PRO THR LEU VAL THR SER PRO PRO GLU VAL SEQRES 10 B 409 TYR HIS LYS VAL VAL PRO GLN ILE PRO VAL LYS SER GLY SEQRES 11 B 409 GLY PRO HIS GLY ALA GLY VAL LEU GLY LEU HIS LEU GLU SEQRES 12 B 409 GLY PRO PHE ILE SER ARG GLU LYS ARG GLY ALA HIS PRO SEQRES 13 B 409 GLU ALA HIS LEU ARG SER PHE GLU ALA ASP ALA PHE GLN SEQRES 14 B 409 ASP LEU LEU ALA THR TYR GLY PRO LEU ASP ASN VAL ARG SEQRES 15 B 409 ILE VAL THR LEU ALA PRO GLU LEU GLY ARG SER HIS GLU SEQRES 16 B 409 VAL ILE ARG ALA LEU THR ALA ARG GLY ILE CYS VAL SER SEQRES 17 B 409 LEU GLY HIS SER VAL ALA ASP LEU ARG ALA ALA GLU ASP SEQRES 18 B 409 ALA VAL TRP SER GLY ALA THR PHE ILE THR HIS LEU PHE SEQRES 19 B 409 ASN ALA MET LEU PRO PHE HIS HIS ARG ASP PRO GLY ILE SEQRES 20 B 409 VAL GLY LEU LEU THR SER ASP ARG LEU PRO ALA GLY ARG SEQRES 21 B 409 CYS ILE PHE TYR GLY MET ILE ALA ASP GLY THR HIS THR SEQRES 22 B 409 ASN PRO ALA ALA LEU ARG ILE ALA HIS ARG ALA HIS PRO SEQRES 23 B 409 GLN GLY LEU VAL LEU VAL THR ASP ALA ILE PRO ALA LEU SEQRES 24 B 409 GLY LEU GLY ASN GLY ARG HIS THR LEU GLY GLN GLN GLU SEQRES 25 B 409 VAL GLU VAL ASP GLY LEU THR ALA TYR VAL ALA GLY THR SEQRES 26 B 409 LYS THR LEU SER GLY SER ILE ALA PRO MET ASP VAL CYS SEQRES 27 B 409 VAL ARG HIS PHE LEU GLN ALA THR GLY CYS SER MET GLU SEQRES 28 B 409 SER ALA LEU GLU ALA ALA SER LEU HIS PRO ALA GLN LEU SEQRES 29 B 409 LEU GLY LEU GLU LYS SER LYS GLY THR LEU ASP PHE GLY SEQRES 30 B 409 ALA ASP ALA ASP PHE VAL VAL LEU ASP ASP SER LEU HIS SEQRES 31 B 409 VAL GLN ALA THR TYR ILE SER GLY GLU LEU VAL TRP GLN SEQRES 32 B 409 ALA ASP ALA ALA ARG GLN HET GLP A 501 28 HET ZN A 502 1 HET GLP B 501 28 HET ZN B 502 1 HETNAM GLP 2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE HETNAM ZN ZINC ION HETSYN GLP GLUCOSAMINE 6-PHOSPHATE; 6-O-PHOSPHONO-ALPHA-D- HETSYN 2 GLP GLUCOSAMINE; 2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D- HETSYN 3 GLP GLUCOSE; 2-AMINO-2-DEOXY-6-O-PHOSPHONO-D-GLUCOSE; 2- HETSYN 4 GLP AMINO-2-DEOXY-6-O-PHOSPHONO-GLUCOSE FORMUL 3 GLP 2(C6 H14 N O8 P) FORMUL 4 ZN 2(ZN 2+) FORMUL 7 HOH *330(H2 O) HELIX 1 AA1 ASP A 40 ARG A 49 1 10 HELIX 2 AA2 ASP A 86 ILE A 98 1 13 HELIX 3 AA3 LEU A 99 HIS A 101 5 3 HELIX 4 AA4 PRO A 114 VAL A 122 1 9 HELIX 5 AA5 PRO A 123 ILE A 125 5 3 HELIX 6 AA6 PRO A 156 LEU A 160 5 5 HELIX 7 AA7 ASP A 166 GLY A 176 1 11 HELIX 8 AA8 ARG A 192 ARG A 203 1 12 HELIX 9 AA9 ASP A 215 GLY A 226 1 12 HELIX 10 AB1 PRO A 245 SER A 253 5 9 HELIX 11 AB2 ASN A 274 HIS A 285 1 12 HELIX 12 AB3 PRO A 334 GLY A 347 1 14 HELIX 13 AB4 SER A 349 ALA A 357 1 9 HELIX 14 AB5 SER A 358 LEU A 365 1 8 HELIX 15 AB6 ASP B 40 GLU B 48 1 9 HELIX 16 AB7 ASP B 86 ILE B 98 1 13 HELIX 17 AB8 LEU B 99 HIS B 101 5 3 HELIX 18 AB9 PRO B 114 VAL B 122 1 9 HELIX 19 AC1 PRO B 123 ILE B 125 5 3 HELIX 20 AC2 PRO B 156 LEU B 160 5 5 HELIX 21 AC3 ALA B 167 GLY B 176 1 10 HELIX 22 AC4 ARG B 192 ARG B 203 1 12 HELIX 23 AC5 ASP B 215 GLY B 226 1 12 HELIX 24 AC6 GLY B 246 SER B 253 5 8 HELIX 25 AC7 ASN B 274 HIS B 285 1 12 HELIX 26 AC8 PRO B 334 GLY B 347 1 14 HELIX 27 AC9 SER B 349 ALA B 357 1 9 HELIX 28 AD1 SER B 358 LEU B 365 1 8 SHEET 1 AA1 4 ARG A 37 ILE A 38 0 SHEET 2 AA1 4 LEU A 31 ARG A 34 -1 N ARG A 34 O ARG A 37 SHEET 3 AA1 4 VAL A 12 THR A 16 -1 N PHE A 15 O LEU A 31 SHEET 4 AA1 4 GLU A 54 ASP A 57 1 O GLU A 54 N GLN A 14 SHEET 1 AA2 6 LYS A 25 ARG A 28 0 SHEET 2 AA2 6 ARG A 19 ARG A 22 -1 N ARG A 22 O LYS A 25 SHEET 3 AA2 6 ILE A 62 PRO A 65 1 O LEU A 63 N ARG A 19 SHEET 4 AA2 6 PHE A 382 LEU A 385 -1 O LEU A 385 N ILE A 62 SHEET 5 AA2 6 VAL A 391 ILE A 396 -1 O GLN A 392 N VAL A 384 SHEET 6 AA2 6 GLU A 399 GLN A 403 -1 O VAL A 401 N THR A 394 SHEET 1 AA3 3 PHE A 67 ILE A 72 0 SHEET 2 AA3 3 VAL A 103 VAL A 111 1 O THR A 109 N ILE A 72 SHEET 3 AA3 3 GLY A 136 VAL A 137 1 O GLY A 136 N THR A 104 SHEET 1 AA4 8 PHE A 67 ILE A 72 0 SHEET 2 AA4 8 VAL A 103 VAL A 111 1 O THR A 109 N ILE A 72 SHEET 3 AA4 8 LEU A 140 GLU A 143 1 O GLU A 143 N LEU A 110 SHEET 4 AA4 8 VAL A 181 LEU A 186 1 O ARG A 182 N LEU A 140 SHEET 5 AA4 8 CYS A 206 LEU A 209 1 O SER A 208 N VAL A 184 SHEET 6 AA4 8 PHE A 229 ILE A 230 1 O PHE A 229 N LEU A 209 SHEET 7 AA4 8 PHE A 263 MET A 266 1 O GLY A 265 N ILE A 230 SHEET 8 AA4 8 LEU A 289 LEU A 291 1 O VAL A 290 N TYR A 264 SHEET 1 AA5 2 GLY A 74 GLY A 75 0 SHEET 2 AA5 2 VAL A 78 ASP A 79 -1 O VAL A 78 N GLY A 75 SHEET 1 AA6 4 GLY A 304 LEU A 308 0 SHEET 2 AA6 4 GLN A 311 ASP A 316 -1 O VAL A 315 N GLY A 304 SHEET 3 AA6 4 THR A 319 VAL A 322 -1 O TYR A 321 N GLU A 314 SHEET 4 AA6 4 LEU A 328 GLY A 330 -1 O SER A 329 N ALA A 320 SHEET 1 AA7 4 ARG B 37 ILE B 38 0 SHEET 2 AA7 4 LEU B 31 ARG B 34 -1 N ARG B 34 O ARG B 37 SHEET 3 AA7 4 LEU B 13 THR B 16 -1 N LEU B 13 O VAL B 33 SHEET 4 AA7 4 GLU B 54 ASP B 57 1 O ARG B 56 N THR B 16 SHEET 1 AA8 6 LYS B 25 ARG B 28 0 SHEET 2 AA8 6 ARG B 19 ARG B 22 -1 N ILE B 20 O LEU B 27 SHEET 3 AA8 6 ILE B 62 PRO B 65 1 O LEU B 63 N ARG B 19 SHEET 4 AA8 6 PHE B 382 LEU B 385 -1 O VAL B 383 N ALA B 64 SHEET 5 AA8 6 VAL B 391 ILE B 396 -1 O GLN B 392 N VAL B 384 SHEET 6 AA8 6 GLU B 399 GLN B 403 -1 O VAL B 401 N THR B 394 SHEET 1 AA9 3 PHE B 67 ILE B 72 0 SHEET 2 AA9 3 VAL B 103 VAL B 111 1 O THR B 109 N ILE B 72 SHEET 3 AA9 3 GLY B 136 VAL B 137 1 O GLY B 136 N THR B 104 SHEET 1 AB1 8 PHE B 67 ILE B 72 0 SHEET 2 AB1 8 VAL B 103 VAL B 111 1 O THR B 109 N ILE B 72 SHEET 3 AB1 8 LEU B 140 GLU B 143 1 O GLU B 143 N LEU B 110 SHEET 4 AB1 8 VAL B 181 LEU B 186 1 O ILE B 183 N LEU B 142 SHEET 5 AB1 8 CYS B 206 LEU B 209 1 O CYS B 206 N ARG B 182 SHEET 6 AB1 8 PHE B 229 ILE B 230 1 O PHE B 229 N LEU B 209 SHEET 7 AB1 8 PHE B 263 MET B 266 1 O GLY B 265 N ILE B 230 SHEET 8 AB1 8 LEU B 289 LEU B 291 1 O VAL B 290 N TYR B 264 SHEET 1 AB2 2 GLY B 74 GLY B 75 0 SHEET 2 AB2 2 VAL B 78 ASP B 79 -1 O VAL B 78 N GLY B 75 SHEET 1 AB3 4 GLY B 304 LEU B 308 0 SHEET 2 AB3 4 GLN B 311 ASP B 316 -1 O VAL B 315 N GLY B 304 SHEET 3 AB3 4 THR B 319 VAL B 322 -1 O TYR B 321 N GLU B 314 SHEET 4 AB3 4 LEU B 328 GLY B 330 -1 O SER B 329 N ALA B 320 LINK OE1 GLU A 143 ZN ZN A 502 1555 1555 1.88 LINK NE2 HIS A 211 ZN ZN A 502 1555 1555 2.05 LINK NE2 HIS A 232 ZN ZN A 502 1555 1555 2.17 LINK ZN ZN A 502 O HOH A 602 1555 1555 1.81 LINK ZN ZN A 502 O HOH A 684 1555 1555 2.27 LINK OE2 GLU B 143 ZN ZN B 502 1555 1555 1.89 LINK NE2 HIS B 211 ZN ZN B 502 1555 1555 2.05 LINK NE2 HIS B 232 ZN ZN B 502 1555 1555 2.19 LINK ZN ZN B 502 O HOH B 601 1555 1555 2.11 LINK ZN ZN B 502 O HOH B 610 1555 1555 2.00 CISPEP 1 GLY A 144 PRO A 145 0 7.83 CISPEP 2 GLY B 144 PRO B 145 0 7.95 CRYST1 63.261 161.449 86.621 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 0.015808 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006194 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011545 0.00000