HEADER ISOMERASE 26-MAR-21 7O0C TITLE HUMAN PHOSPHOMANNOMUTASE 2 (PMM2) WILD-TYPE IN APO STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHOMANNOMUTASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PMM 2; COMPND 5 EC: 5.4.2.8; COMPND 6 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: PMM2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: POPIN-B KEYWDS GLYCOBIOLOGY, CONGENITAL DISORDERS OF GLYCOSYLATION, KEYWDS 2 PHOSPHOTRANSFERASE, PHOSPHOMUTASE, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.RAMON-MAIQUES,A.BRISO-MONTIANO,F.DEL CANO-OCHOA,A.VILAS,B.PEREZ, AUTHOR 2 V.RUBIO REVDAT 3 31-JAN-24 7O0C 1 REMARK REVDAT 2 30-MAR-22 7O0C 1 JRNL REVDAT 1 02-FEB-22 7O0C 0 JRNL AUTH A.BRISO-MONTIANO,F.DEL CANO-OCHOA,A.VILAS, JRNL AUTH 2 A.VELAZQUEZ-CAMPOY,V.RUBIO,B.PEREZ,S.RAMON-MAIQUES JRNL TITL INSIGHT ON MOLECULAR PATHOGENESIS AND PHARMACOCHAPERONING JRNL TITL 2 POTENTIAL IN PHOSPHOMANNOMUTASE 2 DEFICIENCY, PROVIDED BY JRNL TITL 3 NOVEL HUMAN PHOSPHOMANNOMUTASE 2 STRUCTURES. JRNL REF J INHERIT METAB DIS V. 45 318 2022 JRNL REFN ISSN 1573-2665 JRNL PMID 34859900 JRNL DOI 10.1002/JIMD.12461 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.40 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 13643 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 647 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 39.4000 - 4.7900 1.00 2903 158 0.2154 0.2535 REMARK 3 2 4.7900 - 3.8000 0.95 2574 127 0.1833 0.2420 REMARK 3 3 3.8000 - 3.3200 0.87 2314 109 0.2222 0.2476 REMARK 3 4 3.3200 - 3.0200 1.00 2627 126 0.2488 0.3476 REMARK 3 5 3.0200 - 2.8000 1.00 2578 127 0.2901 0.3743 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) : 0.379 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.636 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 66.32 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.34 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 : 0.009 3879 REMARK 3 ANGLE : 1.138 5233 REMARK 3 CHIRALITY : 0.070 565 REMARK 3 PLANARITY : 0.006 687 REMARK 3 DIHEDRAL : 25.750 530 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 7O0C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-MAR-21. REMARK 100 THE DEPOSITION ID IS D_1292114918. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-18 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97912 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13763 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 39.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 17.30 REMARK 200 R MERGE (I) : 0.26500 REMARK 200 R SYM (I) : NULL 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) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 19.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 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: 2AMY REMARK 200 REMARK 200 REMARK: CRYSTALS OF HEXAGONAL MORPHOLOGY AND 0.025 MM IN THE REMARK 200 LARGEST DIMENSION. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DROPS MADE BY MIXING 1 MICROLITER OF REMARK 280 PROTEIN SOLUTION AND 1 MICROLITER OF CRYSTALLIZATION DEPOIT REMARK 280 SOLUTION. PROTEIN SOLUTION CONTAINED 5 MG/ML PROTEIN IN 20 MM REMARK 280 HEPES PH 7.5 AND 0.2 M NACL. CRYSTALLIZATION SOLUTION CONTAINED REMARK 280 0.3-0.4 M MGCL2, 24% PEG3350 AND 0.1 M HEPES PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 240.53400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 120.26700 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 180.40050 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 60.13350 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 300.66750 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 240.53400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 120.26700 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 60.13350 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 180.40050 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 300.66750 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: 2480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 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 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 B 417 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 GLY A -1 REMARK 465 PRO A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 PRO A 4 REMARK 465 GLY B -1 REMARK 465 PRO B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 PRO B 4 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 ARG A 21 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 27 CG CD OE1 OE2 REMARK 470 LYS A 34 CG CD CE NZ REMARK 470 GLU A 62 CG CD OE1 OE2 REMARK 470 LYS A 150 CG CD CE NZ REMARK 470 GLN A 155 CG CD OE1 NE2 REMARK 470 LYS A 156 CG CD CE NZ REMARK 470 ASN A 198 CG OD1 ND2 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 GLU A 235 CG CD OE1 OE2 REMARK 470 ARG B 21 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 27 CG CD OE1 OE2 REMARK 470 GLU B 50 CG CD OE1 OE2 REMARK 470 LYS B 51 CG CD CE NZ REMARK 470 GLU B 54 CG CD OE1 OE2 REMARK 470 LYS B 111 CG CD CE NZ REMARK 470 GLU B 139 CG CD OE1 OE2 REMARK 470 GLU B 146 CG CD OE1 OE2 REMARK 470 LYS B 149 CG CD CE NZ REMARK 470 LYS B 150 CG CD CE NZ REMARK 470 ASN B 152 CG OD1 ND2 REMARK 470 GLN B 155 CG CD OE1 NE2 REMARK 470 LYS B 156 CG CD CE NZ REMARK 470 LYS B 202 CG CD CE NZ REMARK 470 GLU B 235 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 OD1 ASP A 209 O HOH A 401 1.82 REMARK 500 OH TYR B 66 OD1 ASP B 199 2.16 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 CYS A 83 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 LEU B 91 CA - CB - CG ANGL. DEV. = 16.8 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 VAL A 13 -60.06 -99.17 REMARK 500 ASP A 59 28.59 -74.78 REMARK 500 ASN A 71 7.20 56.08 REMARK 500 CYS A 83 112.51 13.66 REMARK 500 ARG A 116 -105.95 -132.05 REMARK 500 THR A 118 73.39 54.72 REMARK 500 SER A 135 4.82 -63.57 REMARK 500 ASP A 185 118.30 -39.21 REMARK 500 ASP A 188 -159.00 -84.38 REMARK 500 ARG B 116 -106.91 -130.12 REMARK 500 THR B 118 67.60 63.18 REMARK 500 MET B 126 146.67 -174.74 REMARK 500 TRP B 187 40.79 -96.39 REMARK 500 ASP B 188 -158.09 -90.84 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 LEU A 82 CYS A 83 137.37 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 MG A 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 12 OD1 REMARK 620 2 ASP A 14 O 110.3 REMARK 620 3 ASP A 209 OD1 92.9 93.6 REMARK 620 4 HOH A 401 O 99.7 130.1 44.8 REMARK 620 5 HOH A 405 O 153.1 80.2 61.1 57.6 REMARK 620 6 HOH A 409 O 106.8 110.8 139.9 96.7 91.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 48 OD2 REMARK 620 2 HOH A 408 O 66.2 REMARK 620 3 HOH A 411 O 72.5 77.4 REMARK 620 4 HOH A 416 O 102.3 78.4 155.2 REMARK 620 5 HOH A 422 O 138.5 155.0 104.1 95.6 REMARK 620 6 HOH A 423 O 136.7 90.9 66.7 108.6 67.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE A 221 O REMARK 620 2 ASP A 223 O 114.7 REMARK 620 3 THR A 226 O 141.9 93.9 REMARK 620 4 THR A 226 OG1 86.6 78.2 74.7 REMARK 620 5 HOH A 414 O 85.2 142.8 86.1 136.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 12 OD1 REMARK 620 2 ASP B 14 O 84.5 REMARK 620 3 ASP B 209 OD1 81.6 85.8 REMARK 620 4 HOH B 401 O 95.3 169.4 83.7 REMARK 620 5 HOH B 409 O 95.6 102.8 170.7 87.7 REMARK 620 6 HOH B 414 O 167.4 105.1 106.7 76.7 74.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PHE B 221 O REMARK 620 2 ASP B 223 O 110.5 REMARK 620 3 THR B 226 O 142.5 106.5 REMARK 620 4 THR B 226 OG1 87.4 89.6 87.2 REMARK 620 5 HOH B 411 O 75.1 141.8 79.6 128.7 REMARK 620 6 HOH B 413 O 77.6 84.3 112.2 160.6 59.3 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2AMY RELATED DB: PDB REMARK 900 INCOMPLETE MODEL WITHOUT COFACTORS AND MISSING LOOPS REMARK 900 RELATED ID: 2Q4R RELATED DB: PDB REMARK 900 INCOMPLETE MODEL WITHOUT COFACTORS AND MISSING LOOPS DBREF 7O0C A 1 246 UNP O15305 PMM2_HUMAN 1 246 DBREF 7O0C B 1 246 UNP O15305 PMM2_HUMAN 1 246 SEQADV 7O0C GLY A -1 UNP O15305 EXPRESSION TAG SEQADV 7O0C PRO A 0 UNP O15305 EXPRESSION TAG SEQADV 7O0C GLY B -1 UNP O15305 EXPRESSION TAG SEQADV 7O0C PRO B 0 UNP O15305 EXPRESSION TAG SEQRES 1 A 248 GLY PRO MET ALA ALA PRO GLY PRO ALA LEU CYS LEU PHE SEQRES 2 A 248 ASP VAL ASP GLY THR LEU THR ALA PRO ARG GLN LYS ILE SEQRES 3 A 248 THR LYS GLU MET ASP ASP PHE LEU GLN LYS LEU ARG GLN SEQRES 4 A 248 LYS ILE LYS ILE GLY VAL VAL GLY GLY SER ASP PHE GLU SEQRES 5 A 248 LYS VAL GLN GLU GLN LEU GLY ASN ASP VAL VAL GLU LYS SEQRES 6 A 248 TYR ASP TYR VAL PHE PRO GLU ASN GLY LEU VAL ALA TYR SEQRES 7 A 248 LYS ASP GLY LYS LEU LEU CYS ARG GLN ASN ILE GLN SER SEQRES 8 A 248 HIS LEU GLY GLU ALA LEU ILE GLN ASP LEU ILE ASN TYR SEQRES 9 A 248 CYS LEU SER TYR ILE ALA LYS ILE LYS LEU PRO LYS LYS SEQRES 10 A 248 ARG GLY THR PHE ILE GLU PHE ARG ASN GLY MET LEU ASN SEQRES 11 A 248 VAL SER PRO ILE GLY ARG SER CYS SER GLN GLU GLU ARG SEQRES 12 A 248 ILE GLU PHE TYR GLU LEU ASP LYS LYS GLU ASN ILE ARG SEQRES 13 A 248 GLN LYS PHE VAL ALA ASP LEU ARG LYS GLU PHE ALA GLY SEQRES 14 A 248 LYS GLY LEU THR PHE SER ILE GLY GLY GLN ILE SER PHE SEQRES 15 A 248 ASP VAL PHE PRO ASP GLY TRP ASP LYS ARG TYR CYS LEU SEQRES 16 A 248 ARG HIS VAL GLU ASN ASP GLY TYR LYS THR ILE TYR PHE SEQRES 17 A 248 PHE GLY ASP LYS THR MET PRO GLY GLY ASN ASP HIS GLU SEQRES 18 A 248 ILE PHE THR ASP PRO ARG THR MET GLY TYR SER VAL THR SEQRES 19 A 248 ALA PRO GLU ASP THR ARG ARG ILE CYS GLU LEU LEU PHE SEQRES 20 A 248 SER SEQRES 1 B 248 GLY PRO MET ALA ALA PRO GLY PRO ALA LEU CYS LEU PHE SEQRES 2 B 248 ASP VAL ASP GLY THR LEU THR ALA PRO ARG GLN LYS ILE SEQRES 3 B 248 THR LYS GLU MET ASP ASP PHE LEU GLN LYS LEU ARG GLN SEQRES 4 B 248 LYS ILE LYS ILE GLY VAL VAL GLY GLY SER ASP PHE GLU SEQRES 5 B 248 LYS VAL GLN GLU GLN LEU GLY ASN ASP VAL VAL GLU LYS SEQRES 6 B 248 TYR ASP TYR VAL PHE PRO GLU ASN GLY LEU VAL ALA TYR SEQRES 7 B 248 LYS ASP GLY LYS LEU LEU CYS ARG GLN ASN ILE GLN SER SEQRES 8 B 248 HIS LEU GLY GLU ALA LEU ILE GLN ASP LEU ILE ASN TYR SEQRES 9 B 248 CYS LEU SER TYR ILE ALA LYS ILE LYS LEU PRO LYS LYS SEQRES 10 B 248 ARG GLY THR PHE ILE GLU PHE ARG ASN GLY MET LEU ASN SEQRES 11 B 248 VAL SER PRO ILE GLY ARG SER CYS SER GLN GLU GLU ARG SEQRES 12 B 248 ILE GLU PHE TYR GLU LEU ASP LYS LYS GLU ASN ILE ARG SEQRES 13 B 248 GLN LYS PHE VAL ALA ASP LEU ARG LYS GLU PHE ALA GLY SEQRES 14 B 248 LYS GLY LEU THR PHE SER ILE GLY GLY GLN ILE SER PHE SEQRES 15 B 248 ASP VAL PHE PRO ASP GLY TRP ASP LYS ARG TYR CYS LEU SEQRES 16 B 248 ARG HIS VAL GLU ASN ASP GLY TYR LYS THR ILE TYR PHE SEQRES 17 B 248 PHE GLY ASP LYS THR MET PRO GLY GLY ASN ASP HIS GLU SEQRES 18 B 248 ILE PHE THR ASP PRO ARG THR MET GLY TYR SER VAL THR SEQRES 19 B 248 ALA PRO GLU ASP THR ARG ARG ILE CYS GLU LEU LEU PHE SEQRES 20 B 248 SER HET MG A 301 1 HET MG A 302 1 HET NA A 303 1 HET MG B 301 1 HET MG B 302 1 HET CL B 303 1 HETNAM MG MAGNESIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 3 MG 4(MG 2+) FORMUL 5 NA NA 1+ FORMUL 8 CL CL 1- FORMUL 9 HOH *41(H2 O) HELIX 1 AA1 THR A 25 GLN A 37 1 13 HELIX 2 AA2 ASP A 48 GLY A 57 1 10 HELIX 3 AA3 ASP A 59 TYR A 64 1 6 HELIX 4 AA4 PRO A 69 LEU A 73 5 5 HELIX 5 AA5 ASN A 86 GLY A 92 1 7 HELIX 6 AA6 GLY A 92 ALA A 108 1 17 HELIX 7 AA7 SER A 137 ASN A 152 1 16 HELIX 8 AA8 ASN A 152 PHE A 165 1 14 HELIX 9 AA9 ASP A 188 GLY A 200 5 13 HELIX 10 AB1 ASP A 217 THR A 222 1 6 HELIX 11 AB2 ALA A 233 SER A 246 1 14 HELIX 12 AB3 THR B 25 ARG B 36 1 12 HELIX 13 AB4 ASP B 48 GLY B 57 1 10 HELIX 14 AB5 ASP B 59 TYR B 64 1 6 HELIX 15 AB6 PRO B 69 LEU B 73 5 5 HELIX 16 AB7 ASN B 86 LYS B 109 1 24 HELIX 17 AB8 SER B 137 ASN B 152 1 16 HELIX 18 AB9 ASN B 152 PHE B 165 1 14 HELIX 19 AC1 ASP B 188 TYR B 191 5 4 HELIX 20 AC2 CYS B 192 GLU B 197 1 6 HELIX 21 AC3 ASP B 217 THR B 222 1 6 HELIX 22 AC4 ALA B 233 SER B 246 1 14 SHEET 1 AA1 7 LYS A 80 LEU A 81 0 SHEET 2 AA1 7 TYR A 76 LYS A 77 -1 N LYS A 77 O LYS A 80 SHEET 3 AA1 7 TYR A 66 PHE A 68 -1 N VAL A 67 O TYR A 76 SHEET 4 AA1 7 LYS A 40 VAL A 44 1 N VAL A 43 O PHE A 68 SHEET 5 AA1 7 ALA A 7 ASP A 12 1 N CYS A 9 O LYS A 40 SHEET 6 AA1 7 THR A 203 GLY A 208 1 O TYR A 205 N LEU A 10 SHEET 7 AA1 7 MET A 227 SER A 230 1 O TYR A 229 N PHE A 206 SHEET 1 AA2 4 ILE A 120 PHE A 122 0 SHEET 2 AA2 4 LEU A 127 VAL A 129 -1 O ASN A 128 N GLU A 121 SHEET 3 AA2 4 SER A 179 PRO A 184 -1 O PHE A 180 N VAL A 129 SHEET 4 AA2 4 LEU A 170 GLY A 175 -1 N SER A 173 O ASP A 181 SHEET 1 AA3 7 LYS B 80 CYS B 83 0 SHEET 2 AA3 7 ALA B 75 LYS B 77 -1 N ALA B 75 O LEU B 82 SHEET 3 AA3 7 TYR B 66 PHE B 68 -1 N VAL B 67 O TYR B 76 SHEET 4 AA3 7 LYS B 40 VAL B 44 1 N VAL B 43 O PHE B 68 SHEET 5 AA3 7 ALA B 7 ASP B 12 1 N PHE B 11 O VAL B 44 SHEET 6 AA3 7 THR B 203 GLY B 208 1 O TYR B 205 N LEU B 8 SHEET 7 AA3 7 MET B 227 SER B 230 1 O MET B 227 N ILE B 204 SHEET 1 AA4 4 ILE B 120 ARG B 123 0 SHEET 2 AA4 4 MET B 126 VAL B 129 -1 O ASN B 128 N GLU B 121 SHEET 3 AA4 4 PHE B 180 PRO B 184 -1 O PHE B 180 N VAL B 129 SHEET 4 AA4 4 LEU B 170 ILE B 174 -1 N THR B 171 O PHE B 183 SSBOND 1 CYS A 83 CYS B 83 1555 8545 2.04 LINK OD1 ASP A 12 MG MG A 301 1555 1555 1.88 LINK O ASP A 14 MG MG A 301 1555 1555 1.92 LINK OD2 ASP A 48 NA NA A 303 1555 1555 2.31 LINK OD1 ASP A 209 MG MG A 301 1555 1555 2.55 LINK O PHE A 221 MG MG A 302 1555 1555 2.52 LINK O ASP A 223 MG MG A 302 1555 1555 2.21 LINK O THR A 226 MG MG A 302 1555 1555 2.04 LINK OG1 THR A 226 MG MG A 302 1555 1555 2.59 LINK MG MG A 301 O HOH A 401 1555 1555 2.09 LINK MG MG A 301 O HOH A 405 1555 1555 2.57 LINK MG MG A 301 O HOH A 409 1555 1555 2.02 LINK MG MG A 302 O HOH A 414 1555 1555 2.79 LINK NA NA A 303 O HOH A 408 1555 1555 2.48 LINK NA NA A 303 O HOH A 411 1555 1555 2.61 LINK NA NA A 303 O HOH A 416 1555 1555 2.68 LINK NA NA A 303 O HOH A 422 1555 1555 2.31 LINK NA NA A 303 O HOH A 423 1555 1555 2.43 LINK OD1 ASP B 12 MG MG B 301 1555 1555 1.85 LINK O ASP B 14 MG MG B 301 1555 1555 2.14 LINK OD1 ASP B 209 MG MG B 301 1555 1555 2.27 LINK O PHE B 221 MG MG B 302 1555 1555 2.82 LINK O ASP B 223 MG MG B 302 1555 1555 2.14 LINK O THR B 226 MG MG B 302 1555 1555 1.94 LINK OG1 THR B 226 MG MG B 302 1555 1555 2.41 LINK MG MG B 301 O HOH B 401 1555 1555 2.23 LINK MG MG B 301 O HOH B 409 1555 1555 2.23 LINK MG MG B 301 O HOH B 414 1555 1555 2.25 LINK MG MG B 302 O HOH B 411 1555 1555 2.76 LINK MG MG B 302 O HOH B 413 1555 1555 2.62 CRYST1 70.582 70.582 360.801 90.00 90.00 120.00 P 65 2 2 24 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 0.014168 0.008180 0.000000 0.00000 SCALE2 0.000000 0.016360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002772 0.00000