HEADER HYDROLASE 22-SEP-13 4MUM TITLE CRYSTAL STRUCTURE OF MITOCHONDRIAL 5'(3')-DEOXY RIBONUCLEOTIDASE TITLE 2 ALTERNATIVE SPLICED VARIANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL 5' NUCLEOTIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 32-233; COMPND 5 SYNONYM: 5'(3')-DEOXYRIBONUCLEOTIDASE; COMPND 6 EC: 3.1.3.-; 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: DNT1, NT5C, UMPH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PMCSG7 KEYWDS 5'-NUCLEOTIDASE, PROTEIN CONFORMATION, SEQUENCE HOMOLOGY, HAD-LIKE, KEYWDS 2 DEPHOSPHORYLATION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.PACHL,P.REZACOVA REVDAT 3 20-SEP-23 4MUM 1 REMARK SEQADV LINK REVDAT 2 28-JAN-15 4MUM 1 JRNL REVDAT 1 26-FEB-14 4MUM 0 JRNL AUTH P.PACHL,M.FABRY,V.VEVERKA,J.BRYNDA,P.REZACOVA JRNL TITL KINETIC AND STRUCTURAL CHARACTERIZATION OF AN ALTERNATIVELY JRNL TITL 2 SPLICED VARIANT OF HUMAN MITOCHONDRIAL JRNL TITL 3 5'(3')-DEOXYRIBONUCLEOTIDASE. JRNL REF J ENZYME INHIB MED CHEM V. 30 63 2015 JRNL REFN ISSN 1475-6366 JRNL PMID 24506201 JRNL DOI 10.3109/14756366.2013.879577 REMARK 2 REMARK 2 RESOLUTION. 1.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 76191 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) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.149 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3809 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) : 1.27 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.30 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4670 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 248 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1607 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 288 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.62 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.33000 REMARK 3 B22 (A**2) : 0.33000 REMARK 3 B33 (A**2) : -0.65000 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): 0.034 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.033 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.019 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.975 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.978 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.973 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1837 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 1762 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2489 ; 2.336 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4074 ; 2.077 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 226 ; 6.010 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 85 ;27.745 ;23.059 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 306 ;11.423 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;16.742 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 267 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2001 ; 0.012 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 422 ; 0.011 ; 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): 836 ; 0.796 ; 1.516 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 837 ; 0.797 ; 1.516 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1049 ; 1.124 ; 2.263 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3596 ; 7.619 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 70 ;28.047 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3777 ; 8.708 ; 5.000 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 : MASK 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 4MUM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082385. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97826 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE, XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76192 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.271 REMARK 200 RESOLUTION RANGE LOW (A) : 46.656 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.60800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 4L6A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 MM POTASSIUM PHOSPHATE MONOBASIC, REMARK 280 8% PEG8000, 10% GYCEROL, PH 4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 53.33600 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 36.68600 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 36.68600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 80.00400 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 36.68600 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 36.68600 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.66800 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 36.68600 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.68600 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 80.00400 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 36.68600 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.68600 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.66800 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 53.33600 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: 9840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 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 350 BIOMT1 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 53.33600 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 A 579 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 ALA A 29 REMARK 465 ALA A 30 REMARK 465 SER A 31 REMARK 465 GLY A 32 REMARK 465 GLY A 33 REMARK 465 LYS A 183 REMARK 465 TRP A 184 REMARK 465 PRO A 185 REMARK 465 ALA A 186 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 34 NE CZ NH1 NH2 REMARK 470 GLU A 70 CD OE1 OE2 REMARK 470 LYS A 99 NZ REMARK 470 LYS A 134 NZ REMARK 470 GLN A 211 CG CD OE1 NE2 REMARK 470 ARG A 214 NE CZ NH1 NH2 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 SER A 131 N TRS A 314 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 144 CE1 TYR A 144 CZ -0.132 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 ARG A 37 NE - CZ - NH1 ANGL. DEV. = 3.6 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 MET A 42 -72.61 -98.98 REMARK 500 VAL A 45 -52.76 -127.38 REMARK 500 ASN A 100 -1.68 73.11 REMARK 500 THR A 181 1.26 177.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PEG A 311 REMARK 610 PEG A 312 REMARK 610 PG4 A 313 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 41 OD2 REMARK 620 2 ASP A 43 O 86.5 REMARK 620 3 ASP A 176 OD1 83.7 90.4 REMARK 620 4 PO4 A 302 O2 87.4 93.7 169.9 REMARK 620 5 HOH A 401 O 172.9 87.3 92.9 96.4 REMARK 620 6 HOH A 402 O 90.9 177.4 89.8 85.7 95.3 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 MG A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 313 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A 314 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 315 DBREF 4MUM A 32 233 UNP Q2I378 Q2I378_HUMAN 32 233 SEQADV 4MUM SER A 27 UNP Q2I378 EXPRESSION TAG SEQADV 4MUM ASN A 28 UNP Q2I378 EXPRESSION TAG SEQADV 4MUM ALA A 29 UNP Q2I378 EXPRESSION TAG SEQADV 4MUM ALA A 30 UNP Q2I378 EXPRESSION TAG SEQADV 4MUM SER A 31 UNP Q2I378 EXPRESSION TAG SEQRES 1 A 207 SER ASN ALA ALA SER GLY GLY ARG ALA LEU ARG VAL LEU SEQRES 2 A 207 VAL ASP MET ASP GLY VAL LEU ALA ASP PHE GLU GLY GLY SEQRES 3 A 207 PHE LEU ARG LYS PHE ARG ALA ARG PHE PRO ASP GLN PRO SEQRES 4 A 207 PHE ILE ALA LEU GLU ASP ARG ARG GLY PHE TRP VAL SER SEQRES 5 A 207 GLU GLN TYR GLY ARG LEU ARG PRO GLY LEU SER GLU LYS SEQRES 6 A 207 ALA ILE SER ILE TRP GLU SER LYS ASN PHE PHE PHE GLU SEQRES 7 A 207 LEU GLU PRO LEU PRO GLY ALA VAL GLU ALA VAL LYS GLU SEQRES 8 A 207 MET ALA SER LEU GLN ASN THR ASP VAL PHE ILE CYS THR SEQRES 9 A 207 SER PRO ILE LYS MET PHE LYS TYR CYS PRO TYR GLU LYS SEQRES 10 A 207 TYR ALA TRP VAL GLU LYS TYR PHE GLY PRO ASP PHE LEU SEQRES 11 A 207 GLU GLN ILE VAL LEU THR ARG ASP LYS THR VAL VAL SER SEQRES 12 A 207 ALA ASP LEU LEU ILE ASP ASP ARG PRO ASP ILE THR GLY SEQRES 13 A 207 LYS TRP PRO ALA THR GLY ALA GLU PRO THR PRO SER TRP SEQRES 14 A 207 GLU HIS VAL LEU PHE THR ALA CYS HIS ASN GLN HIS LEU SEQRES 15 A 207 GLN LEU GLN PRO PRO ARG ARG ARG LEU HIS SER TRP ALA SEQRES 16 A 207 ASP ASP TRP LYS ALA ILE LEU ASP SER LYS ARG PRO HET MG A 301 1 HET PO4 A 302 5 HET GOL A 303 6 HET GOL A 304 6 HET GOL A 305 12 HET GOL A 306 6 HET GOL A 307 6 HET GOL A 308 6 HET GOL A 309 6 HET GOL A 310 6 HET PEG A 311 6 HET PEG A 312 4 HET PG4 A 313 4 HET TRS A 314 8 HET CL A 315 1 HETNAM MG MAGNESIUM ION HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 2 MG MG 2+ FORMUL 3 PO4 O4 P 3- FORMUL 4 GOL 8(C3 H8 O3) FORMUL 12 PEG 2(C4 H10 O3) FORMUL 14 PG4 C8 H18 O5 FORMUL 15 TRS C4 H12 N O3 1+ FORMUL 16 CL CL 1- FORMUL 17 HOH *288(H2 O) HELIX 1 1 ASP A 48 PHE A 61 1 14 HELIX 2 2 ALA A 68 ARG A 72 5 5 HELIX 3 3 TRP A 76 ARG A 85 1 10 HELIX 4 4 GLY A 87 GLU A 97 1 11 HELIX 5 5 GLY A 110 LEU A 121 1 12 HELIX 6 6 TYR A 138 GLY A 152 1 15 HELIX 7 7 PRO A 153 GLU A 157 5 5 HELIX 8 8 ASP A 164 VAL A 168 5 5 HELIX 9 9 ASP A 223 SER A 230 1 8 SHEET 1 A 6 ILE A 159 LEU A 161 0 SHEET 2 A 6 THR A 124 THR A 130 1 N ILE A 128 O VAL A 160 SHEET 3 A 6 LEU A 36 VAL A 40 1 N LEU A 36 O ASP A 125 SHEET 4 A 6 LEU A 172 ASP A 175 1 O LEU A 172 N LEU A 39 SHEET 5 A 6 GLU A 196 PHE A 200 1 O VAL A 198 N LEU A 173 SHEET 6 A 6 ARG A 215 LEU A 217 1 O LEU A 217 N LEU A 199 LINK OD2 ASP A 41 MG MG A 301 1555 1555 2.09 LINK O ASP A 43 MG MG A 301 1555 1555 2.07 LINK OD1 ASP A 176 MG MG A 301 1555 1555 2.05 LINK MG MG A 301 O2 PO4 A 302 1555 1555 2.12 LINK MG MG A 301 O HOH A 401 1555 1555 2.02 LINK MG MG A 301 O HOH A 402 1555 1555 2.06 CISPEP 1 PRO A 212 PRO A 213 0 9.07 SITE 1 AC1 6 ASP A 41 ASP A 43 ASP A 176 PO4 A 302 SITE 2 AC1 6 HOH A 401 HOH A 402 SITE 1 AC2 13 ASP A 41 MET A 42 ASP A 43 THR A 130 SITE 2 AC2 13 SER A 131 LYS A 143 LYS A 165 MG A 301 SITE 3 AC2 13 GOL A 303 TRS A 314 HOH A 401 HOH A 402 SITE 4 AC2 13 HOH A 408 SITE 1 AC3 10 PHE A 49 GLU A 50 PHE A 75 HIS A 204 SITE 2 AC3 10 PO4 A 302 GOL A 305 TRS A 314 HOH A 401 SITE 3 AC3 10 HOH A 457 HOH A 645 SITE 1 AC4 10 ASN A 100 PHE A 103 LYS A 137 TYR A 141 SITE 2 AC4 10 PEG A 311 HOH A 431 HOH A 504 HOH A 580 SITE 3 AC4 10 HOH A 583 HOH A 610 SITE 1 AC5 12 PHE A 49 PHE A 75 TRP A 76 VAL A 77 SITE 2 AC5 12 TRP A 96 ILE A 133 GOL A 303 GOL A 306 SITE 3 AC5 12 TRS A 314 HOH A 449 HOH A 548 HOH A 645 SITE 1 AC6 8 TRP A 96 GLU A 97 ILE A 133 LYS A 134 SITE 2 AC6 8 MET A 135 GOL A 305 HOH A 548 HOH A 614 SITE 1 AC7 8 SER A 27 ASN A 28 ALA A 119 THR A 124 SITE 2 AC7 8 ASP A 125 VAL A 126 GLN A 158 HOH A 508 SITE 1 AC8 8 ASP A 48 GLY A 51 GLY A 52 ARG A 55 SITE 2 AC8 8 GLU A 106 PG4 A 313 CL A 315 HOH A 629 SITE 1 AC9 9 GLY A 110 GLU A 113 ALA A 114 TRP A 220 SITE 2 AC9 9 ALA A 221 ASP A 222 TRP A 224 HOH A 485 SITE 3 AC9 9 HOH A 575 SITE 1 BC1 13 ASP A 48 LEU A 69 GLU A 90 ALA A 202 SITE 2 BC1 13 CYS A 203 HOH A 418 HOH A 419 HOH A 457 SITE 3 BC1 13 HOH A 474 HOH A 536 HOH A 582 HOH A 687 SITE 4 BC1 13 HOH A 688 SITE 1 BC2 9 PHE A 103 LYS A 149 PRO A 213 ARG A 214 SITE 2 BC2 9 ARG A 215 GOL A 304 HOH A 463 HOH A 593 SITE 3 BC2 9 HOH A 610 SITE 1 BC3 6 PRO A 132 ILE A 133 LYS A 134 LEU A 156 SITE 2 BC3 6 ARG A 163 HOH A 550 SITE 1 BC4 8 ASP A 48 LYS A 91 GLU A 106 PRO A 107 SITE 2 BC4 8 LEU A 108 PRO A 109 GOL A 308 HOH A 475 SITE 1 BC5 15 ASP A 43 PHE A 49 PHE A 75 SER A 131 SITE 2 BC5 15 PRO A 132 ILE A 133 ARG A 163 PO4 A 302 SITE 3 BC5 15 GOL A 303 GOL A 305 HOH A 408 HOH A 585 SITE 4 BC5 15 HOH A 644 HOH A 645 HOH A 647 SITE 1 BC6 6 ASP A 48 GLY A 52 LEU A 105 GLU A 106 SITE 2 BC6 6 GOL A 308 HOH A 432 CRYST1 73.372 73.372 106.672 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 0.013629 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013629 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009375 0.00000