HEADER IMMUNE SYSTEM 25-APR-13 4KDT TITLE STRUCTURE OF AN EARLY NATIVE-LIKE INTERMEDIATE OF BETA2-MICROGLOBULIN TITLE 2 AMYLOIDOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NANOBODY24; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: BETA-2-MICROGLOBULIN; COMPND 8 CHAIN: C, D; COMPND 9 FRAGMENT: UNP RESIDUES 21-119; COMPND 10 SYNONYM: BETA-2-MICROGLOBULIN FORM PI 5.3; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAMELIDAE; SOURCE 3 ORGANISM_TAXID: 9835; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHEN6C; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: B2M, CDABP0092, HDCMA22P; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) PLYSS; SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET11A KEYWDS IMMUNOGLOBULIN FOLD, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR S.VANDERHAEGEN,M.FISLAGE,E.PARDON,W.VERSEES,J.STEYAERT REVDAT 4 20-SEP-23 4KDT 1 REMARK SEQADV REVDAT 3 15-NOV-17 4KDT 1 REMARK REVDAT 2 23-OCT-13 4KDT 1 JRNL REVDAT 1 28-AUG-13 4KDT 0 JRNL AUTH S.VANDERHAEGEN,M.FISLAGE,K.DOMANSKA,W.VERSEES,E.PARDON, JRNL AUTH 2 V.BELLOTTI,J.STEYAERT JRNL TITL STRUCTURE OF AN EARLY NATIVE-LIKE INTERMEDIATE OF BETA JRNL TITL 2 2-MICROGLOBULIN AMYLOIDOGENESIS. JRNL REF PROTEIN SCI. V. 22 1349 2013 JRNL REFN ISSN 0961-8368 JRNL PMID 23904325 JRNL DOI 10.1002/PRO.2321 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24016 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1264 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1744 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.4040 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.4320 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3564 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 50 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.84000 REMARK 3 B22 (A**2) : -0.84000 REMARK 3 B33 (A**2) : 1.69000 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): 0.376 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.283 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3715 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3336 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5032 ; 1.550 ; 1.939 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7659 ; 3.657 ; 3.003 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 448 ; 7.371 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 192 ;35.611 ;23.594 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 605 ;17.179 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;19.742 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 521 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4247 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 928 ; 0.009 ; 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): 1783 ; 1.622 ; 2.293 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1782 ; 1.622 ; 2.293 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2222 ; 2.767 ; 3.430 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1932 ; 2.383 ; 2.626 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): 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 129 REMARK 3 ORIGIN FOR THE GROUP (A): 49.5590 35.5750 67.1770 REMARK 3 T TENSOR REMARK 3 T11: 0.4392 T22: 0.1579 REMARK 3 T33: 0.0279 T12: 0.0416 REMARK 3 T13: 0.0276 T23: 0.0179 REMARK 3 L TENSOR REMARK 3 L11: 2.0948 L22: 3.6903 REMARK 3 L33: 3.2536 L12: 0.7319 REMARK 3 L13: -0.4714 L23: -0.5561 REMARK 3 S TENSOR REMARK 3 S11: 0.0039 S12: -0.1223 S13: -0.0405 REMARK 3 S21: 0.1874 S22: -0.0853 S23: 0.0665 REMARK 3 S31: 0.1382 S32: -0.0744 S33: 0.0813 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 128 REMARK 3 ORIGIN FOR THE GROUP (A): 47.3090 35.3620 42.1960 REMARK 3 T TENSOR REMARK 3 T11: 0.4619 T22: 0.1962 REMARK 3 T33: 0.0399 T12: -0.0556 REMARK 3 T13: 0.0125 T23: -0.0310 REMARK 3 L TENSOR REMARK 3 L11: 1.7875 L22: 3.5495 REMARK 3 L33: 3.2887 L12: -0.3514 REMARK 3 L13: -0.4686 L23: 0.2366 REMARK 3 S TENSOR REMARK 3 S11: -0.0509 S12: 0.1581 S13: -0.0202 REMARK 3 S21: -0.3243 S22: -0.0557 S23: -0.0623 REMARK 3 S31: 0.1734 S32: 0.0171 S33: 0.1065 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 4 C 97 REMARK 3 ORIGIN FOR THE GROUP (A): 48.2670 14.3560 24.4680 REMARK 3 T TENSOR REMARK 3 T11: 0.5057 T22: 0.3283 REMARK 3 T33: 0.2752 T12: 0.0274 REMARK 3 T13: 0.0554 T23: -0.1024 REMARK 3 L TENSOR REMARK 3 L11: 3.0007 L22: 4.0618 REMARK 3 L33: 12.6098 L12: -1.0273 REMARK 3 L13: -0.5328 L23: 4.3596 REMARK 3 S TENSOR REMARK 3 S11: 0.1684 S12: 0.1304 S13: 0.1259 REMARK 3 S21: 0.1794 S22: -0.3311 S23: 0.2172 REMARK 3 S31: -0.2837 S32: -0.4050 S33: 0.1627 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 3 D 97 REMARK 3 ORIGIN FOR THE GROUP (A): 48.5070 14.4290 85.1030 REMARK 3 T TENSOR REMARK 3 T11: 0.4958 T22: 0.2928 REMARK 3 T33: 0.2383 T12: -0.0560 REMARK 3 T13: 0.0615 T23: 0.0591 REMARK 3 L TENSOR REMARK 3 L11: 2.4701 L22: 3.9656 REMARK 3 L33: 10.1847 L12: 0.5770 REMARK 3 L13: 0.4583 L23: -3.7638 REMARK 3 S TENSOR REMARK 3 S11: 0.0621 S12: -0.1107 S13: 0.0197 REMARK 3 S21: -0.3856 S22: -0.3341 S23: -0.2157 REMARK 3 S31: 0.0467 S32: 0.2473 S33: 0.2719 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 4KDT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-APR-13. REMARK 100 THE DEPOSITION ID IS D_1000079212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97950 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25281 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.30 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 14.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.010 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 2X89 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 66.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, 1.6 M MGSO4, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 48.39500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.39500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 83.89500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.39500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.39500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 83.89500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.39500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.39500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 83.89500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.39500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.39500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 83.89500 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 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, D 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12000 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 C2 GOL C 102 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 HIS A 130 REMARK 465 HIS A 131 REMARK 465 HIS A 132 REMARK 465 HIS A 133 REMARK 465 HIS A 134 REMARK 465 HIS B 129 REMARK 465 HIS B 130 REMARK 465 HIS B 131 REMARK 465 HIS B 132 REMARK 465 HIS B 133 REMARK 465 HIS B 134 REMARK 465 MET C 0 REMARK 465 ILE C 1 REMARK 465 GLN C 2 REMARK 465 ARG C 3 REMARK 465 ALA C 15 REMARK 465 ASP C 98 REMARK 465 MET C 99 REMARK 465 MET D 0 REMARK 465 ILE D 1 REMARK 465 GLN D 2 REMARK 465 ASP D 98 REMARK 465 MET D 99 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 SER A 128 -162.34 -78.86 REMARK 500 SER B 30 34.75 38.13 REMARK 500 VAL B 108 123.01 -35.53 REMARK 500 ALA B 109 -71.68 -45.59 REMARK 500 HIS C 31 70.30 62.36 REMARK 500 ASP C 96 -80.98 -94.33 REMARK 500 HIS D 31 80.11 67.82 REMARK 500 ASP D 96 -66.21 -124.47 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 HIS C 13 PRO C 14 149.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN A 3 -15.78 REMARK 500 GLN A 3 -15.68 REMARK 500 GLN A 13 10.25 REMARK 500 GLN A 13 12.11 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL C 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL D 102 DBREF 4KDT C 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 4KDT D 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 4KDT A 1 134 PDB 4KDT 4KDT 1 134 DBREF 4KDT B 1 134 PDB 4KDT 4KDT 1 134 SEQADV 4KDT MET C 0 UNP P61769 EXPRESSION TAG SEQADV 4KDT GLY C 32 UNP P61769 PRO 52 ENGINEERED MUTATION SEQADV 4KDT MET D 0 UNP P61769 EXPRESSION TAG SEQADV 4KDT GLY D 32 UNP P61769 PRO 52 ENGINEERED MUTATION SEQRES 1 A 134 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 A 134 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 A 134 TYR THR ASP SER ARG TYR CYS MET ALA TRP PHE ARG GLN SEQRES 4 A 134 ALA PRO GLY LYS GLU ARG GLU TRP VAL ALA ARG ILE ASN SEQRES 5 A 134 SER GLY ARG ASP ILE THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 A 134 GLY ARG PHE THR PHE SER GLN ASP ASN ALA LYS ASN THR SEQRES 7 A 134 VAL TYR LEU GLN MET ASP SER LEU GLU PRO GLU ASP THR SEQRES 8 A 134 ALA THR TYR TYR CYS ALA THR ASP ILE PRO LEU ARG CYS SEQRES 9 A 134 ARG ASP ILE VAL ALA LYS GLY GLY ASP GLY PHE ARG TYR SEQRES 10 A 134 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HIS HIS SEQRES 11 A 134 HIS HIS HIS HIS SEQRES 1 B 134 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY SER VAL GLN SEQRES 2 B 134 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 B 134 TYR THR ASP SER ARG TYR CYS MET ALA TRP PHE ARG GLN SEQRES 4 B 134 ALA PRO GLY LYS GLU ARG GLU TRP VAL ALA ARG ILE ASN SEQRES 5 B 134 SER GLY ARG ASP ILE THR TYR TYR ALA ASP SER VAL LYS SEQRES 6 B 134 GLY ARG PHE THR PHE SER GLN ASP ASN ALA LYS ASN THR SEQRES 7 B 134 VAL TYR LEU GLN MET ASP SER LEU GLU PRO GLU ASP THR SEQRES 8 B 134 ALA THR TYR TYR CYS ALA THR ASP ILE PRO LEU ARG CYS SEQRES 9 B 134 ARG ASP ILE VAL ALA LYS GLY GLY ASP GLY PHE ARG TYR SEQRES 10 B 134 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HIS HIS SEQRES 11 B 134 HIS HIS HIS HIS SEQRES 1 C 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 C 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 C 100 TYR VAL SER GLY PHE HIS GLY SER ASP ILE GLU VAL ASP SEQRES 4 C 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 C 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 C 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 C 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 C 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 D 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 D 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 D 100 TYR VAL SER GLY PHE HIS GLY SER ASP ILE GLU VAL ASP SEQRES 4 D 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 D 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 D 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 D 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 D 100 LYS ILE VAL LYS TRP ASP ARG ASP MET HET SO4 A 201 5 HET SO4 A 202 5 HET SO4 A 203 5 HET SO4 B 201 5 HET SO4 C 101 5 HET GOL C 102 6 HET SO4 D 101 5 HET GOL D 102 6 HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 SO4 6(O4 S 2-) FORMUL 10 GOL 2(C3 H8 O3) FORMUL 13 HOH *50(H2 O) HELIX 1 1 TYR A 27 ARG A 31 5 5 HELIX 2 2 ASP A 62 LYS A 65 5 4 HELIX 3 3 GLU A 87 THR A 91 5 5 HELIX 4 4 ILE A 100 ARG A 105 1 6 HELIX 5 5 TYR B 27 ARG B 31 5 5 HELIX 6 6 ASP B 62 LYS B 65 5 4 HELIX 7 7 GLU B 87 THR B 91 5 5 HELIX 8 8 ILE B 100 ASP B 106 1 7 SHEET 1 A 4 GLN A 3 SER A 7 0 SHEET 2 A 4 LEU A 18 SER A 25 -1 O ALA A 23 N GLN A 5 SHEET 3 A 4 VAL A 79 MET A 83 -1 O VAL A 79 N CYS A 22 SHEET 4 A 4 PHE A 68 GLN A 72 -1 N THR A 69 O GLN A 82 SHEET 1 B 6 GLY A 10 GLN A 13 0 SHEET 2 B 6 THR A 122 SER A 127 1 O THR A 125 N GLY A 10 SHEET 3 B 6 ALA A 92 ASP A 99 -1 N TYR A 94 O THR A 122 SHEET 4 B 6 CYS A 33 GLN A 39 -1 N PHE A 37 O TYR A 95 SHEET 5 B 6 ARG A 45 ILE A 51 -1 O VAL A 48 N TRP A 36 SHEET 6 B 6 THR A 58 TYR A 60 -1 O TYR A 59 N ARG A 50 SHEET 1 C 4 GLY A 10 GLN A 13 0 SHEET 2 C 4 THR A 122 SER A 127 1 O THR A 125 N GLY A 10 SHEET 3 C 4 ALA A 92 ASP A 99 -1 N TYR A 94 O THR A 122 SHEET 4 C 4 TYR A 117 TRP A 118 -1 O TYR A 117 N THR A 98 SHEET 1 D 4 GLN B 3 SER B 7 0 SHEET 2 D 4 LEU B 18 SER B 25 -1 O ALA B 23 N GLN B 5 SHEET 3 D 4 VAL B 79 MET B 83 -1 O VAL B 79 N CYS B 22 SHEET 4 D 4 PHE B 68 GLN B 72 -1 N SER B 71 O TYR B 80 SHEET 1 E 6 GLY B 10 GLN B 13 0 SHEET 2 E 6 THR B 122 SER B 127 1 O THR B 125 N GLY B 10 SHEET 3 E 6 ALA B 92 ASP B 99 -1 N TYR B 94 O THR B 122 SHEET 4 E 6 CYS B 33 GLN B 39 -1 N PHE B 37 O TYR B 95 SHEET 5 E 6 GLU B 46 ILE B 51 -1 O VAL B 48 N TRP B 36 SHEET 6 E 6 THR B 58 TYR B 60 -1 O TYR B 59 N ARG B 50 SHEET 1 F 4 GLY B 10 GLN B 13 0 SHEET 2 F 4 THR B 122 SER B 127 1 O THR B 125 N GLY B 10 SHEET 3 F 4 ALA B 92 ASP B 99 -1 N TYR B 94 O THR B 122 SHEET 4 F 4 TYR B 117 TRP B 118 -1 O TYR B 117 N THR B 98 SHEET 1 G 4 LYS C 6 SER C 11 0 SHEET 2 G 4 ASN C 21 PHE C 30 -1 O ASN C 24 N TYR C 10 SHEET 3 G 4 SER C 61 PHE C 70 -1 O LEU C 64 N VAL C 27 SHEET 4 G 4 GLU C 50 PHE C 56 -1 N GLU C 50 O TYR C 67 SHEET 1 H 4 GLU C 44 ARG C 45 0 SHEET 2 H 4 GLU C 36 LYS C 41 -1 N LYS C 41 O GLU C 44 SHEET 3 H 4 TYR C 78 ASN C 83 -1 O ALA C 79 N LEU C 40 SHEET 4 H 4 LYS C 91 LYS C 94 -1 O VAL C 93 N CYS C 80 SHEET 1 I 4 LYS D 6 SER D 11 0 SHEET 2 I 4 ASN D 21 PHE D 30 -1 O SER D 28 N LYS D 6 SHEET 3 I 4 SER D 61 PHE D 70 -1 O LEU D 64 N VAL D 27 SHEET 4 I 4 GLU D 50 PHE D 56 -1 N GLU D 50 O TYR D 67 SHEET 1 J 4 GLU D 44 ARG D 45 0 SHEET 2 J 4 GLU D 36 LYS D 41 -1 N LYS D 41 O GLU D 44 SHEET 3 J 4 TYR D 78 ASN D 83 -1 O ALA D 79 N LEU D 40 SHEET 4 J 4 LYS D 91 LYS D 94 -1 O VAL D 93 N CYS D 80 SSBOND 1 CYS A 22 CYS A 96 1555 1555 2.07 SSBOND 2 CYS A 33 CYS A 104 1555 1555 2.05 SSBOND 3 CYS B 22 CYS B 96 1555 1555 2.06 SSBOND 4 CYS B 33 CYS B 104 1555 1555 2.05 SSBOND 5 CYS C 25 CYS C 80 1555 1555 2.07 SSBOND 6 CYS D 25 CYS D 80 1555 1555 2.06 SITE 1 AC1 5 ASP A 106 ILE A 107 GLY A 112 ASP A 113 SITE 2 AC1 5 GLY A 114 SITE 1 AC2 5 TYR A 59 LYS A 65 LYS A 110 HOH A 306 SITE 2 AC2 5 LYS D 94 SITE 1 AC3 3 SER A 25 GLY A 26 SER A 30 SITE 1 AC4 4 TYR B 59 LYS B 65 LYS B 110 LYS C 94 SITE 1 AC5 4 ARG B 31 SER B 53 ARG C 45 ARG C 81 SITE 1 AC6 1 ARG C 12 SITE 1 AC7 3 ARG A 31 ARG D 45 ARG D 81 SITE 1 AC8 3 TYR D 26 SER D 52 TYR D 63 CRYST1 96.790 96.790 167.790 90.00 90.00 90.00 P 42 21 2 16 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 0.010332 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010332 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005960 0.00000