HEADER PROTEIN BINDING 10-MAR-06 2GBR TITLE CRYSTAL STRUCTURE OF THE 35-36 MOAD INSERTION MUTANT OF UBIQUITIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: UBIQUITIN; COMPND 3 CHAIN: A, B, C; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRS KEYWDS LOOP INSERTION, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR D.M.FERRARO,D.J.FERRARO,S.RAMASWAMY,A.D.ROBERTSON REVDAT 4 30-AUG-23 2GBR 1 REMARK SEQADV LINK REVDAT 3 18-OCT-17 2GBR 1 REMARK REVDAT 2 24-FEB-09 2GBR 1 VERSN REVDAT 1 16-MAY-06 2GBR 0 JRNL AUTH D.M.FERRARO,D.J.FERRARO,S.RAMASWAMY,A.D.ROBERTSON JRNL TITL STRUCTURES OF UBIQUITIN INSERTION MUTANTS SUPPORT JRNL TITL 2 SITE-SPECIFIC REFLEX RESPONSE TO INSERTIONS HYPOTHESIS. JRNL REF J.MOL.BIOL. V. 359 390 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16647719 JRNL DOI 10.1016/J.JMB.2006.03.047 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 4.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 14668 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 745 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.04 REMARK 3 REFLECTION IN BIN (WORKING SET) : 918 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.90 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.2900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1840 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 189 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.69 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : 0.02000 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): 0.262 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.226 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.151 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.539 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1864 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1292 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2515 ; 1.237 ; 1.982 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3188 ; 0.795 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 227 ; 5.667 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 83 ;41.294 ;25.542 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 372 ;15.577 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;15.311 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 299 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1995 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 325 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 350 ; 0.213 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1277 ; 0.179 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 822 ; 0.168 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1044 ; 0.083 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 131 ; 0.256 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 7 ; 0.243 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 30 ; 0.442 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 83 ; 0.202 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 40 ; 0.243 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.493 ; 0.200 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): 1485 ; 0.838 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 460 ; 0.142 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1864 ; 0.965 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 809 ; 1.775 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 651 ; 2.746 ; 4.500 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): 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2GBR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00808 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SI(111) REMARK 200 DOUBLE-CRYSTAL SYSTEM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : JDIRECTOR REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.5LDZ REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14696 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 5.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.860 REMARK 200 R MERGE (I) : 0.13500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.42100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 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: PDB ENTRY 2GBM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24-30% PEG 4000, 50-80 MM CADMIUM REMARK 280 CHLORIDE, 100 MM SODIUM ACETATE, PH 3.9, VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 22.23250 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.31350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 27.40350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.31350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 22.23250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 27.40350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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 300 REMARK: THE MONOMER IS BELIEVED TO BE THE ACTIVE BIOLOGICAL REMARK 300 ASSEMBLY. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -85.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 -1.000000 0.000000 0.000000 22.23250 REMARK 350 BIOMT2 1 0.000000 -1.000000 0.000000 109.61400 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 46.31350 REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, C REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8940 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 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 LEU A 78 REMARK 465 ARG A 79 REMARK 465 GLY A 80 REMARK 465 GLY A 81 REMARK 465 LEU B 78 REMARK 465 ARG B 79 REMARK 465 GLY B 80 REMARK 465 GLY B 81 REMARK 465 ARG C 77 REMARK 465 LEU C 78 REMARK 465 ARG C 79 REMARK 465 GLY C 80 REMARK 465 GLY C 81 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 OE1 GLN C 67 O HOH C 335 2.11 REMARK 500 OD1 ASP B 63 O HOH B 313 2.15 REMARK 500 NZ LYS C 27 OD1 ASP C 57 2.15 REMARK 500 O HOH B 335 O HOH B 363 2.16 REMARK 500 OE2 GLU A 56 O HOH A 351 2.16 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 OE1 GLU B 56 OE2 GLU C 16 4576 2.03 REMARK 500 OE1 GLU A 56 OE2 GLU B 16 3545 2.08 REMARK 500 O HOH A 324 O HOH B 335 3545 2.14 REMARK 500 O HOH A 337 O HOH C 359 3545 2.18 REMARK 500 OE2 GLU B 69 O HOH A 336 3555 2.19 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 PRO C 43 4.51 -69.85 REMARK 500 LYS C 68 126.03 -39.88 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 CD B 301 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 18 OE2 REMARK 620 2 GLU A 18 OE1 52.2 REMARK 620 3 ASP B 21 OD2 122.2 154.6 REMARK 620 4 ASP B 21 OD1 93.7 100.5 54.1 REMARK 620 5 HOH B 315 O 131.6 80.4 95.6 84.7 REMARK 620 6 HOH B 318 O 98.6 111.0 94.1 147.3 108.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD C 302 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 21 OD1 REMARK 620 2 ASP A 21 OD2 54.8 REMARK 620 3 GLU C 18 OE1 113.9 168.4 REMARK 620 4 GLU C 18 OE2 94.8 121.3 53.4 REMARK 620 5 HOH C 313 O 148.3 93.5 97.8 104.3 REMARK 620 6 HOH C 332 O 87.4 95.1 86.1 136.5 95.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 306 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 24 OE1 REMARK 620 2 GLU A 24 OE2 53.9 REMARK 620 3 ASP A 57 OD2 102.0 86.0 REMARK 620 4 HOH A 317 O 101.4 152.8 88.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 313 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 32 OD1 REMARK 620 2 HOH A 328 O 87.6 REMARK 620 3 HOH A 347 O 69.7 141.4 REMARK 620 4 HOH B 347 O 88.3 161.2 52.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD A 308 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 63 OD1 REMARK 620 2 ASP A 63 OD2 54.8 REMARK 620 3 HOH A 337 O 104.5 103.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD C 305 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 68 NZ REMARK 620 2 GLU C 56 OE2 112.7 REMARK 620 3 HOH C 316 O 152.7 86.0 REMARK 620 4 HOH C 333 O 108.4 89.1 90.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 309 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 316 O REMARK 620 2 HOH B 314 O 108.5 REMARK 620 3 HOH B 330 O 167.3 79.0 REMARK 620 4 HOH C 312 O 106.1 112.8 79.4 REMARK 620 5 HOH C 318 O 76.4 164.1 93.7 79.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 311 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 320 O REMARK 620 2 HOH A 334 O 106.1 REMARK 620 3 HOH B 320 O 121.5 99.0 REMARK 620 4 HOH B 341 O 105.8 110.4 113.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 312 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 321 O REMARK 620 2 LYS B 6 NZ 129.5 REMARK 620 3 HOH B 351 O 137.3 93.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 303 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 18 OE1 REMARK 620 2 GLU B 18 OE2 53.3 REMARK 620 3 ASP C 21 OD2 117.4 164.2 REMARK 620 4 ASP C 21 OD1 90.0 110.9 53.9 REMARK 620 5 HOH C 311 O 106.9 101.3 93.7 147.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 307 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 24 OE1 REMARK 620 2 ASP B 57 OD2 88.2 REMARK 620 3 HOH B 332 O 150.7 84.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD B 304 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 32 OD1 REMARK 620 2 HOH B 342 O 95.4 REMARK 620 3 HOH C 316 O 166.9 97.7 REMARK 620 4 HOH C 333 O 92.4 89.5 88.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CD C 310 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 326 O REMARK 620 2 ASP C 63 OD2 88.9 REMARK 620 3 ASP C 63 OD1 89.7 53.2 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD C 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD C 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD C 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD B 312 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD A 313 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GBJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 9-10 8 GLYCINE INSERTION MUTANT OF REMARK 900 UBIQUITIN REMARK 900 RELATED ID: 2GBK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 9-10 MOAD INSERTION MUTANT OF THE SAME REMARK 900 PROTEIN REMARK 900 RELATED ID: 2GBM RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE INSERTION MUTANT OF THE REMARK 900 SAME PROTEIN REMARK 900 RELATED ID: 2GBN RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE 35-36 8 GLYCINE INSERTION MUTANT OF REMARK 900 UBIQUITIN DBREF 2GBR A 1 81 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2GBR B 1 81 UNP P62988 UBIQ_HUMAN 1 76 DBREF 2GBR C 1 81 UNP P62988 UBIQ_HUMAN 1 76 SEQADV 2GBR ARG A 36 UNP P62988 INSERTION SEQADV 2GBR TRP A 37 UNP P62988 INSERTION SEQADV 2GBR ALA A 38 UNP P62988 INSERTION SEQADV 2GBR LEU A 39 UNP P62988 INSERTION SEQADV 2GBR ALA A 40 UNP P62988 INSERTION SEQADV 2GBR ARG B 36 UNP P62988 INSERTION SEQADV 2GBR TRP B 37 UNP P62988 INSERTION SEQADV 2GBR ALA B 38 UNP P62988 INSERTION SEQADV 2GBR LEU B 39 UNP P62988 INSERTION SEQADV 2GBR ALA B 40 UNP P62988 INSERTION SEQADV 2GBR ARG C 36 UNP P62988 INSERTION SEQADV 2GBR TRP C 37 UNP P62988 INSERTION SEQADV 2GBR ALA C 38 UNP P62988 INSERTION SEQADV 2GBR LEU C 39 UNP P62988 INSERTION SEQADV 2GBR ALA C 40 UNP P62988 INSERTION SEQRES 1 A 81 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 A 81 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 A 81 LYS ALA LYS ILE GLN ASP LYS GLU GLY ARG TRP ALA LEU SEQRES 4 A 81 ALA ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY SEQRES 5 A 81 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN SEQRES 6 A 81 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 7 A 81 ARG GLY GLY SEQRES 1 B 81 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 B 81 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 B 81 LYS ALA LYS ILE GLN ASP LYS GLU GLY ARG TRP ALA LEU SEQRES 4 B 81 ALA ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY SEQRES 5 B 81 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN SEQRES 6 B 81 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 7 B 81 ARG GLY GLY SEQRES 1 C 81 MET GLN ILE PHE VAL LYS THR LEU THR GLY LYS THR ILE SEQRES 2 C 81 THR LEU GLU VAL GLU PRO SER ASP THR ILE GLU ASN VAL SEQRES 3 C 81 LYS ALA LYS ILE GLN ASP LYS GLU GLY ARG TRP ALA LEU SEQRES 4 C 81 ALA ILE PRO PRO ASP GLN GLN ARG LEU ILE PHE ALA GLY SEQRES 5 C 81 LYS GLN LEU GLU ASP GLY ARG THR LEU SER ASP TYR ASN SEQRES 6 C 81 ILE GLN LYS GLU SER THR LEU HIS LEU VAL LEU ARG LEU SEQRES 7 C 81 ARG GLY GLY HET CD A 306 1 HET CD A 308 1 HET CD A 313 1 HET CD B 301 1 HET CD B 303 1 HET CD B 304 1 HET CD B 307 1 HET CD B 309 1 HET CD B 311 1 HET CD B 312 1 HET CD C 302 1 HET CD C 305 1 HET CD C 310 1 HETNAM CD CADMIUM ION FORMUL 4 CD 13(CD 2+) FORMUL 17 HOH *189(H2 O) HELIX 1 1 THR A 22 GLU A 34 1 13 HELIX 2 2 GLY A 35 ILE A 41 5 7 HELIX 3 3 PRO A 42 ASP A 44 5 3 HELIX 4 4 LEU A 61 ASN A 65 5 5 HELIX 5 5 THR B 22 GLU B 34 1 13 HELIX 6 6 GLY B 35 ILE B 41 5 7 HELIX 7 7 PRO B 42 ASP B 44 5 3 HELIX 8 8 LEU B 61 ASN B 65 5 5 HELIX 9 9 THR C 22 GLU C 34 1 13 HELIX 10 10 GLY C 35 ALA C 40 1 6 HELIX 11 11 LEU C 61 ASN C 65 5 5 SHEET 1 A 5 THR A 12 GLU A 16 0 SHEET 2 A 5 GLN A 2 LYS A 6 -1 N ILE A 3 O LEU A 15 SHEET 3 A 5 THR A 71 LEU A 76 1 O LEU A 74 N LYS A 6 SHEET 4 A 5 GLN A 46 PHE A 50 -1 N ARG A 47 O VAL A 75 SHEET 5 A 5 LYS A 53 GLN A 54 -1 O LYS A 53 N PHE A 50 SHEET 1 B 5 THR B 12 GLU B 16 0 SHEET 2 B 5 GLN B 2 LYS B 6 -1 N ILE B 3 O LEU B 15 SHEET 3 B 5 THR B 71 LEU B 76 1 O LEU B 74 N LYS B 6 SHEET 4 B 5 GLN B 46 PHE B 50 -1 N ARG B 47 O VAL B 75 SHEET 5 B 5 LYS B 53 GLN B 54 -1 O LYS B 53 N PHE B 50 SHEET 1 C 5 THR C 12 GLU C 16 0 SHEET 2 C 5 GLN C 2 LYS C 6 -1 N VAL C 5 O ILE C 13 SHEET 3 C 5 THR C 71 VAL C 75 1 O LEU C 72 N PHE C 4 SHEET 4 C 5 ARG C 47 PHE C 50 -1 N ILE C 49 O HIS C 73 SHEET 5 C 5 LYS C 53 GLN C 54 -1 O LYS C 53 N PHE C 50 LINK OE2 GLU A 18 CD CD B 301 2575 1555 2.54 LINK OE1 GLU A 18 CD CD B 301 2575 1555 2.47 LINK OD1 ASP A 21 CD CD C 302 2575 1555 2.22 LINK OD2 ASP A 21 CD CD C 302 2575 1555 2.55 LINK OE1 GLU A 24 CD CD A 306 1555 1555 2.26 LINK OE2 GLU A 24 CD CD A 306 1555 1555 2.57 LINK OD1 ASP A 32 CD CD A 313 1555 1555 2.24 LINK OD2 ASP A 57 CD CD A 306 1555 1555 2.61 LINK OD1 ASP A 63 CD CD A 308 1555 1555 2.43 LINK OD2 ASP A 63 CD CD A 308 1555 1555 2.33 LINK NZ LYS A 68 CD CD C 305 3655 1555 1.75 LINK CD CD A 306 O HOH A 317 1555 1555 2.19 LINK CD CD A 308 O HOH A 337 1555 1555 2.29 LINK CD CD A 313 O HOH A 328 1555 1555 2.37 LINK CD CD A 313 O HOH A 347 1555 1555 2.60 LINK CD CD A 313 O HOH B 347 1555 3645 2.97 LINK O HOH A 316 CD CD B 309 2575 1555 2.54 LINK O HOH A 320 CD CD B 311 1555 1555 2.42 LINK O HOH A 321 CD CD B 312 1555 1555 2.17 LINK O HOH A 334 CD CD B 311 1555 1555 2.78 LINK NZ LYS B 6 CD CD B 312 1555 1555 3.10 LINK OE1 GLU B 18 CD CD B 303 1555 1555 2.57 LINK OE2 GLU B 18 CD CD B 303 1555 1555 2.29 LINK OD2 ASP B 21 CD CD B 301 1555 1555 2.47 LINK OD1 ASP B 21 CD CD B 301 1555 1555 2.34 LINK OE1 GLU B 24 CD CD B 307 1555 1555 2.50 LINK OD1 ASP B 32 CD CD B 304 1555 1555 2.15 LINK OD2 ASP B 57 CD CD B 307 1555 1555 2.12 LINK CD CD B 301 O HOH B 315 1555 1555 2.33 LINK CD CD B 301 O HOH B 318 1555 1555 2.26 LINK CD CD B 303 OD2 ASP C 21 1555 1555 2.54 LINK CD CD B 303 OD1 ASP C 21 1555 1555 2.33 LINK CD CD B 303 O HOH C 311 1555 1555 2.29 LINK CD CD B 304 O HOH B 342 1555 1555 2.53 LINK CD CD B 304 O HOH C 316 1555 4476 2.67 LINK CD CD B 304 O HOH C 333 1555 4476 2.49 LINK CD CD B 307 O HOH B 332 1555 1555 1.87 LINK CD CD B 309 O HOH B 314 1555 1555 2.52 LINK CD CD B 309 O HOH B 330 1555 1555 2.66 LINK CD CD B 309 O HOH C 312 1555 1555 2.46 LINK CD CD B 309 O HOH C 318 1555 1555 3.10 LINK CD CD B 311 O HOH B 320 1555 1555 2.52 LINK CD CD B 311 O HOH B 341 1555 1555 2.53 LINK CD CD B 312 O HOH B 351 1555 1555 2.56 LINK O HOH B 326 CD CD C 310 4576 1555 2.57 LINK OE1 GLU C 18 CD CD C 302 1555 1555 2.49 LINK OE2 GLU C 18 CD CD C 302 1555 1555 2.45 LINK OE2 GLU C 56 CD CD C 305 1555 1555 2.19 LINK OD2 ASP C 63 CD CD C 310 1555 1555 2.46 LINK OD1 ASP C 63 CD CD C 310 1555 1555 2.52 LINK CD CD C 302 O HOH C 313 1555 1555 2.32 LINK CD CD C 302 O HOH C 332 1555 1555 1.66 LINK CD CD C 305 O HOH C 316 1555 1555 2.55 LINK CD CD C 305 O HOH C 333 1555 1555 2.48 SITE 1 AC1 4 GLU A 18 ASP B 21 HOH B 315 HOH B 318 SITE 1 AC2 4 ASP A 21 GLU C 18 HOH C 313 HOH C 332 SITE 1 AC3 3 GLU B 18 ASP C 21 HOH C 311 SITE 1 AC4 5 ASP B 32 HOH B 342 CD C 305 HOH C 316 SITE 2 AC4 5 HOH C 333 SITE 1 AC5 5 LYS A 68 CD B 304 GLU C 56 HOH C 316 SITE 2 AC5 5 HOH C 333 SITE 1 AC6 3 GLU A 24 ASP A 57 HOH A 317 SITE 1 AC7 3 GLU B 24 ASP B 57 HOH B 332 SITE 1 AC8 2 ASP A 63 HOH A 337 SITE 1 AC9 4 HOH A 316 HOH B 314 HOH B 330 HOH C 312 SITE 1 BC1 2 HOH B 326 ASP C 63 SITE 1 BC2 4 HOH A 320 HOH A 334 HOH B 320 HOH B 341 SITE 1 BC3 3 HOH A 321 LYS B 6 HOH B 351 SITE 1 BC4 6 ASP A 32 HOH A 328 HOH A 347 GLU B 56 SITE 2 BC4 6 HOH B 347 LYS C 68 CRYST1 44.465 54.807 92.627 90.00 90.00 90.00 P 21 21 21 12 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 0.022490 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018246 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010796 0.00000