HEADER DNA BINDING PROTEIN 28-MAY-18 5ZYW TITLE THE CRYSTAL STRUCTURE OF APO-HSMGME1 WITH MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL GENOME MAINTENANCE EXONUCLEASE 1; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.-.-; COMPND 5 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: MGME1, C20ORF72, DDK1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS HUAMNMGME1, DNA COMPLEX, DNA EXONUCLEASE, DNA BINDING PROTEIN, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.YANG,J.GAN REVDAT 6 22-NOV-23 5ZYW 1 LINK REVDAT 5 28-AUG-19 5ZYW 1 TITLE REVDAT 4 23-JAN-19 5ZYW 1 TITLE REVDAT 3 28-NOV-18 5ZYW 1 JRNL REVDAT 2 31-OCT-18 5ZYW 1 JRNL REVDAT 1 19-SEP-18 5ZYW 0 JRNL AUTH C.YANG,R.WU,H.LIU,Y.CHEN,Y.GAO,X.CHEN,Y.LI,J.MA,J.LI,J.GAN JRNL TITL STRUCTURAL INSIGHTS INTO DNA DEGRADATION BY HUMAN JRNL TITL 2 MITOCHONDRIAL NUCLEASE MGME1 JRNL REF NUCLEIC ACIDS RES. V. 46 11075 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 30247721 JRNL DOI 10.1093/NAR/GKY855 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 12836 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 681 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 526 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 55.11 REMARK 3 BIN R VALUE (WORKING SET) : 0.2690 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1854 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 19 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.03000 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): 0.324 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.225 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.186 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.517 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.923 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1913 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1790 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2594 ; 1.113 ; 1.963 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4120 ; 0.849 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 230 ; 5.434 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;31.726 ;24.941 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 324 ;13.748 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;15.160 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 288 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2137 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 433 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 929 ; 1.253 ; 3.482 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 928 ; 1.254 ; 3.484 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1156 ; 2.260 ; 5.206 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1157 ; 2.259 ; 5.204 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 984 ; 0.963 ; 3.501 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 984 ; 0.963 ; 3.501 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1439 ; 1.766 ; 5.219 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2200 ; 4.093 ;26.955 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2160 ; 4.001 ;26.939 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 REMARK 4 REMARK 4 5ZYW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-MAY-18. REMARK 100 THE DEPOSITION ID IS D_1300007845. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NFPSS REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14320 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 21.60 REMARK 200 R MERGE (I) : 0.10500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 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 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: PHASER REMARK 200 STARTING MODEL: 5ZYT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.35 M DI-SODIUM TARTRATE, 21% PEG REMARK 280 3350 AND 0.1 M MNCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.42050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 33.99850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 33.99850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 86.13075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 33.99850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 33.99850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 28.71025 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 33.99850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 33.99850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 86.13075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 33.99850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 33.99850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.71025 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 57.42050 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 220 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 KCAL/MOL 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 GLY A 91 REMARK 465 GLU A 92 REMARK 465 ASP A 93 REMARK 465 ARG A 94 REMARK 465 ARG A 95 REMARK 465 VAL A 96 REMARK 465 PRO A 97 REMARK 465 ASN A 113 REMARK 465 ALA A 114 REMARK 465 SER A 115 REMARK 465 ASP A 116 REMARK 465 PRO A 117 REMARK 465 GLN A 190 REMARK 465 GLU A 191 REMARK 465 THR A 192 REMARK 465 LEU A 193 REMARK 465 LYS A 194 REMARK 465 GLU A 195 REMARK 465 ARG A 196 REMARK 465 ASP A 197 REMARK 465 GLU A 198 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 GLN A 98 CB CG CD OE1 NE2 REMARK 470 ASN A 99 CG OD1 ND2 REMARK 470 ARG A 108 CG CD NE CZ NH1 NH2 REMARK 470 SER A 109 OG REMARK 470 ASP A 110 CG OD1 OD2 REMARK 470 LYS A 111 CG CD CE NZ REMARK 470 PRO A 112 CG CD REMARK 470 ARG A 155 NE CZ NH1 NH2 REMARK 470 LYS A 202 CG CD CE NZ REMARK 470 GLU A 229 CG CD OE1 OE2 REMARK 470 GLN A 290 CG CD OE1 NE2 REMARK 470 GLN A 316 OE1 NE2 REMARK 470 GLU A 330 CG CD OE1 OE2 REMARK 470 LYS A 332 CG CD CE NZ REMARK 470 GLN A 335 CG CD OE1 NE2 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 PRO A 112 C - N - CA ANGL. DEV. = 12.0 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 ASN A 99 45.44 -92.03 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 403 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 134 OG1 REMARK 620 2 SER A 343 OG 78.3 REMARK 620 3 HOH A 501 O 87.4 164.2 REMARK 620 4 HOH A 504 O 90.2 93.7 79.7 REMARK 620 5 HOH A 550 O 94.4 102.0 85.5 164.3 REMARK 620 6 HOH A 577 O 170.8 93.0 100.9 87.6 90.0 REMARK 620 N 1 2 3 4 5 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 HIS A 180 NE2 REMARK 620 2 ASP A 238 OD2 90.9 REMARK 620 3 ASP A 251 OD1 177.1 88.5 REMARK 620 4 TRP A 252 O 90.7 114.5 86.9 REMARK 620 5 TLA A 404 O1 78.5 97.3 104.4 146.6 REMARK 620 6 TLA A 404 O11 90.1 151.9 91.7 93.6 55.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 238 OD1 REMARK 620 2 GLU A 344 OE2 167.7 REMARK 620 3 TLA A 404 O1 92.0 98.5 REMARK 620 4 HOH A 511 O 85.5 83.9 177.3 REMARK 620 5 HOH A 528 O 89.0 83.6 95.7 83.3 REMARK 620 6 HOH A 554 O 97.5 88.9 90.5 90.8 170.9 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 MN 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 MN A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TLA A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 405 DBREF 5ZYW A 91 344 UNP Q9BQP7 MGME1_HUMAN 91 344 SEQRES 1 A 254 GLY GLU ASP ARG ARG VAL PRO GLN ASN TRP PHE PRO ILE SEQRES 2 A 254 PHE ASN PRO GLU ARG SER ASP LYS PRO ASN ALA SER ASP SEQRES 3 A 254 PRO SER VAL PRO LEU LYS ILE PRO LEU GLN ARG ASN VAL SEQRES 4 A 254 ILE PRO SER VAL THR ARG VAL LEU GLN GLN THR MET THR SEQRES 5 A 254 LYS GLN GLN VAL PHE LEU LEU GLU ARG TRP LYS GLN ARG SEQRES 6 A 254 MET ILE LEU GLU LEU GLY GLU ASP GLY PHE LYS GLU TYR SEQRES 7 A 254 THR SER ASN VAL PHE LEU GLN GLY LYS ARG PHE HIS GLU SEQRES 8 A 254 ALA LEU GLU SER ILE LEU SER PRO GLN GLU THR LEU LYS SEQRES 9 A 254 GLU ARG ASP GLU ASN LEU LEU LYS SER GLY TYR ILE GLU SEQRES 10 A 254 SER VAL GLN HIS ILE LEU LYS ASP VAL SER GLY VAL ARG SEQRES 11 A 254 ALA LEU GLU SER ALA VAL GLN HIS GLU THR LEU ASN TYR SEQRES 12 A 254 ILE GLY LEU LEU ASP CYS VAL ALA GLU TYR GLN GLY LYS SEQRES 13 A 254 LEU CYS VAL ILE ASP TRP LYS THR SER GLU LYS PRO LYS SEQRES 14 A 254 PRO PHE ILE GLN SER THR PHE ASP ASN PRO LEU GLN VAL SEQRES 15 A 254 VAL ALA TYR MET GLY ALA MET ASN HIS ASP THR ASN TYR SEQRES 16 A 254 SER PHE GLN VAL GLN CYS GLY LEU ILE VAL VAL ALA TYR SEQRES 17 A 254 LYS ASP GLY SER PRO ALA HIS PRO HIS PHE MET ASP ALA SEQRES 18 A 254 GLU LEU CYS SER GLN TYR TRP THR LYS TRP LEU LEU ARG SEQRES 19 A 254 LEU GLU GLU TYR THR GLU LYS LYS LYS ASN GLN ASN ILE SEQRES 20 A 254 GLN LYS PRO GLU TYR SER GLU HET MN A 401 1 HET MN A 402 1 HET MN A 403 1 HET TLA A 404 10 HET GOL A 405 6 HETNAM MN MANGANESE (II) ION HETNAM TLA L(+)-TARTARIC ACID HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 MN 3(MN 2+) FORMUL 5 TLA C4 H6 O6 FORMUL 6 GOL C3 H8 O3 FORMUL 7 HOH *94(H2 O) HELIX 1 AA1 SER A 132 THR A 140 1 9 HELIX 2 AA2 THR A 142 LEU A 187 1 46 HELIX 3 AA3 SER A 203 VAL A 209 1 7 HELIX 4 AA4 VAL A 209 LYS A 214 1 6 HELIX 5 AA5 SER A 264 PHE A 266 5 3 HELIX 6 AA6 ASP A 267 HIS A 281 1 15 HELIX 7 AA7 ASP A 310 GLU A 330 1 21 SHEET 1 AA1 5 VAL A 216 GLN A 227 0 SHEET 2 AA1 5 ILE A 234 TYR A 243 -1 O GLU A 242 N SER A 217 SHEET 3 AA1 5 LYS A 246 THR A 254 -1 O ILE A 250 N CYS A 239 SHEET 4 AA1 5 CYS A 291 ALA A 297 1 O ALA A 297 N LYS A 253 SHEET 5 AA1 5 HIS A 305 MET A 309 -1 O MET A 309 N GLY A 292 LINK OG1 THR A 134 MN MN A 403 1555 1555 2.47 LINK NE2 HIS A 180 MN MN A 402 1555 1555 2.34 LINK OD1 ASP A 238 MN MN A 401 1555 1555 2.07 LINK OD2 ASP A 238 MN MN A 402 1555 1555 2.11 LINK OD1 ASP A 251 MN MN A 402 1555 1555 2.18 LINK O TRP A 252 MN MN A 402 1555 1555 2.11 LINK OG SER A 343 MN MN A 403 1555 1555 2.34 LINK OE2 GLU A 344 MN MN A 401 1555 1555 2.13 LINK MN MN A 401 O1 TLA A 404 1555 1555 2.15 LINK MN MN A 401 O HOH A 511 1555 1555 2.15 LINK MN MN A 401 O HOH A 528 1555 1555 2.28 LINK MN MN A 401 O HOH A 554 1555 1555 2.03 LINK MN MN A 402 O1 TLA A 404 1555 1555 2.28 LINK MN MN A 402 O11 TLA A 404 1555 1555 2.40 LINK MN MN A 403 O HOH A 501 1555 1555 2.68 LINK MN MN A 403 O HOH A 504 1555 7555 2.67 LINK MN MN A 403 O HOH A 550 1555 1555 2.44 LINK MN MN A 403 O HOH A 577 1555 7555 2.35 SITE 1 AC1 6 ASP A 238 GLU A 344 TLA A 404 HOH A 511 SITE 2 AC1 6 HOH A 528 HOH A 554 SITE 1 AC2 5 HIS A 180 ASP A 238 ASP A 251 TRP A 252 SITE 2 AC2 5 TLA A 404 SITE 1 AC3 7 THR A 134 LYS A 259 SER A 343 HOH A 501 SITE 2 AC3 7 HOH A 504 HOH A 550 HOH A 577 SITE 1 AC4 16 THR A 134 HIS A 180 ASP A 238 ASP A 251 SITE 2 AC4 16 TRP A 252 LYS A 253 GLN A 263 GLN A 271 SITE 3 AC4 16 GLU A 344 MN A 401 MN A 402 HOH A 501 SITE 4 AC4 16 HOH A 504 HOH A 538 HOH A 554 HOH A 561 SITE 1 AC5 5 THR A 265 ASN A 268 PRO A 269 ILE A 294 SITE 2 AC5 5 HIS A 307 CRYST1 67.997 67.997 114.841 90.00 90.00 90.00 P 43 21 2 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 0.014707 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014707 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008708 0.00000